Multiple sequence alignment - TraesCS4A01G226800

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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 TraesCS4A01G226800 chr4A 100.000 3206 0 0 1 3206 535033849 535037054 0.000000e+00 5921.0
1 TraesCS4A01G226800 chr4B 90.777 3036 127 51 240 3206 90893928 90890977 0.000000e+00 3914.0
2 TraesCS4A01G226800 chr4B 91.000 200 2 7 46 239 90894162 90893973 4.100000e-64 255.0
3 TraesCS4A01G226800 chr4D 90.130 3009 95 64 240 3202 61850752 61853604 0.000000e+00 3725.0
4 TraesCS4A01G226800 chr4D 88.211 246 4 8 3 239 61850477 61850706 1.470000e-68 270.0
5 TraesCS4A01G226800 chr5A 82.653 196 34 0 1843 2038 459775651 459775456 1.180000e-39 174.0
6 TraesCS4A01G226800 chr5A 79.459 185 32 6 1839 2020 443289623 443289804 3.360000e-25 126.0
7 TraesCS4A01G226800 chr5A 87.500 80 8 2 1354 1432 443289054 443289132 1.220000e-14 91.6
8 TraesCS4A01G226800 chr5B 80.435 184 32 4 1839 2020 401667829 401668010 1.550000e-28 137.0
9 TraesCS4A01G226800 chr5B 77.564 156 25 9 1354 1501 401667251 401667404 5.700000e-13 86.1
10 TraesCS4A01G226800 chr5D 79.891 184 33 4 1839 2020 342175354 342175535 7.220000e-27 132.0
11 TraesCS4A01G226800 chr5D 76.374 182 31 11 1328 1501 342174761 342174938 1.580000e-13 87.9
12 TraesCS4A01G226800 chr1B 77.907 172 38 0 1846 2017 667750250 667750421 1.220000e-19 108.0
13 TraesCS4A01G226800 chr1D 77.326 172 39 0 1846 2017 479540798 479540969 5.660000e-18 102.0
14 TraesCS4A01G226800 chr1A 75.581 172 42 0 1846 2017 575808298 575808469 5.700000e-13 86.1


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 TraesCS4A01G226800 chr4A 535033849 535037054 3205 False 5921.0 5921 100.0000 1 3206 1 chr4A.!!$F1 3205
1 TraesCS4A01G226800 chr4B 90890977 90894162 3185 True 2084.5 3914 90.8885 46 3206 2 chr4B.!!$R1 3160
2 TraesCS4A01G226800 chr4D 61850477 61853604 3127 False 1997.5 3725 89.1705 3 3202 2 chr4D.!!$F1 3199

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
574 662 0.169672 CTTCCTGCATCTTGTTGCGG 59.83 55.0 5.72 5.72 45.77 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2327 0.550914 ACACCAGGGCTTCTTTGTGA 59.449 50.0 0.0 0.0 32.75 3.58 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
18 19 1.533753 CCTGGCTGCCTTTGGGAAA 60.534 57.895 21.03 0.00 33.58 3.13
19 20 1.538687 CCTGGCTGCCTTTGGGAAAG 61.539 60.000 21.03 5.82 38.24 2.62
133 136 1.155424 TGACAAACACCGAGGTTCGC 61.155 55.000 0.00 0.00 38.82 4.70
156 159 3.290710 TGCTTTTGGTCTCTTCTTGCTT 58.709 40.909 0.00 0.00 0.00 3.91
157 160 3.067180 TGCTTTTGGTCTCTTCTTGCTTG 59.933 43.478 0.00 0.00 0.00 4.01
158 161 3.636381 CTTTTGGTCTCTTCTTGCTTGC 58.364 45.455 0.00 0.00 0.00 4.01
159 162 2.645838 TTGGTCTCTTCTTGCTTGCT 57.354 45.000 0.00 0.00 0.00 3.91
160 163 2.175878 TGGTCTCTTCTTGCTTGCTC 57.824 50.000 0.00 0.00 0.00 4.26
161 164 1.417517 TGGTCTCTTCTTGCTTGCTCA 59.582 47.619 0.00 0.00 0.00 4.26
162 165 1.803555 GGTCTCTTCTTGCTTGCTCAC 59.196 52.381 0.00 0.00 0.00 3.51
163 166 1.803555 GTCTCTTCTTGCTTGCTCACC 59.196 52.381 0.00 0.00 0.00 4.02
164 167 1.163554 CTCTTCTTGCTTGCTCACCC 58.836 55.000 0.00 0.00 0.00 4.61
165 168 0.767375 TCTTCTTGCTTGCTCACCCT 59.233 50.000 0.00 0.00 0.00 4.34
166 169 1.163554 CTTCTTGCTTGCTCACCCTC 58.836 55.000 0.00 0.00 0.00 4.30
202 207 0.998945 CCCCTCTCTCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
203 208 0.478507 CCCTCTCTCTCCTCCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
204 209 0.478507 CCTCTCTCTCCTCCTCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
233 243 1.155042 GCAGTGCAGGACAAGAAGAG 58.845 55.000 11.09 0.00 0.00 2.85
234 244 1.270518 GCAGTGCAGGACAAGAAGAGA 60.271 52.381 11.09 0.00 0.00 3.10
374 431 4.913355 TGGTCCATACATTAGTCCATCCAT 59.087 41.667 0.00 0.00 0.00 3.41
375 432 5.013079 TGGTCCATACATTAGTCCATCCATC 59.987 44.000 0.00 0.00 0.00 3.51
379 436 3.475566 ACATTAGTCCATCCATCCACG 57.524 47.619 0.00 0.00 0.00 4.94
382 439 0.752658 TAGTCCATCCATCCACGCAG 59.247 55.000 0.00 0.00 0.00 5.18
416 486 3.117171 CAGCTCGCTCGCTTGCTT 61.117 61.111 3.45 0.00 38.41 3.91
417 487 2.813042 AGCTCGCTCGCTTGCTTC 60.813 61.111 0.87 0.00 36.74 3.86
466 550 3.147595 CTCGCATCCACGGGAGGA 61.148 66.667 8.51 2.62 41.09 3.71
467 551 3.144120 CTCGCATCCACGGGAGGAG 62.144 68.421 8.51 5.57 41.90 3.69
468 552 3.461773 CGCATCCACGGGAGGAGT 61.462 66.667 8.51 0.00 41.90 3.85
469 553 2.187946 GCATCCACGGGAGGAGTG 59.812 66.667 8.51 4.56 41.90 3.51
489 577 0.456628 GAGTAACCCCTCACTCGCTC 59.543 60.000 0.00 0.00 32.49 5.03
490 578 1.139095 GTAACCCCTCACTCGCTCG 59.861 63.158 0.00 0.00 0.00 5.03
491 579 2.707849 TAACCCCTCACTCGCTCGC 61.708 63.158 0.00 0.00 0.00 5.03
493 581 4.200283 CCCCTCACTCGCTCGCTC 62.200 72.222 0.00 0.00 0.00 5.03
494 582 4.544689 CCCTCACTCGCTCGCTCG 62.545 72.222 0.00 0.00 0.00 5.03
496 584 4.172772 CTCACTCGCTCGCTCGCT 62.173 66.667 0.00 0.00 0.00 4.93
497 585 4.167359 TCACTCGCTCGCTCGCTC 62.167 66.667 0.00 0.00 0.00 5.03
545 633 4.662179 ACTGTTCATCATCCATCCTACCAT 59.338 41.667 0.00 0.00 0.00 3.55
548 636 4.151943 TCATCATCCATCCTACCATCCT 57.848 45.455 0.00 0.00 0.00 3.24
567 655 2.025510 CCTTCCTTCCTTCCTGCATCTT 60.026 50.000 0.00 0.00 0.00 2.40
574 662 0.169672 CTTCCTGCATCTTGTTGCGG 59.830 55.000 5.72 5.72 45.77 5.69
598 686 2.035321 GAGTACAGCAGCTACCCATCTC 59.965 54.545 0.00 0.00 0.00 2.75
607 695 2.703007 AGCTACCCATCTCCTAAAGCTG 59.297 50.000 0.00 0.00 37.44 4.24
608 696 2.700897 GCTACCCATCTCCTAAAGCTGA 59.299 50.000 0.00 0.00 0.00 4.26
611 699 3.663198 ACCCATCTCCTAAAGCTGATCT 58.337 45.455 0.00 0.00 0.00 2.75
614 702 3.903090 CCATCTCCTAAAGCTGATCTCCT 59.097 47.826 0.00 0.00 0.00 3.69
615 703 4.021192 CCATCTCCTAAAGCTGATCTCCTC 60.021 50.000 0.00 0.00 0.00 3.71
616 704 3.571590 TCTCCTAAAGCTGATCTCCTCC 58.428 50.000 0.00 0.00 0.00 4.30
617 705 3.206412 TCTCCTAAAGCTGATCTCCTCCT 59.794 47.826 0.00 0.00 0.00 3.69
618 706 3.966665 CTCCTAAAGCTGATCTCCTCCTT 59.033 47.826 0.00 0.00 0.00 3.36
619 707 4.366267 TCCTAAAGCTGATCTCCTCCTTT 58.634 43.478 0.00 0.00 0.00 3.11
620 708 4.163078 TCCTAAAGCTGATCTCCTCCTTTG 59.837 45.833 0.00 0.00 0.00 2.77
621 709 2.416680 AAGCTGATCTCCTCCTTTGC 57.583 50.000 0.00 0.00 0.00 3.68
624 712 2.308275 AGCTGATCTCCTCCTTTGCTTT 59.692 45.455 0.00 0.00 0.00 3.51
625 713 3.087781 GCTGATCTCCTCCTTTGCTTTT 58.912 45.455 0.00 0.00 0.00 2.27
626 714 4.018960 AGCTGATCTCCTCCTTTGCTTTTA 60.019 41.667 0.00 0.00 0.00 1.52
706 794 1.336125 GCAGGAGCAGGATATTGTTGC 59.664 52.381 0.00 0.33 41.58 4.17
708 796 0.947244 GGAGCAGGATATTGTTGCGG 59.053 55.000 0.00 0.00 42.47 5.69
710 798 1.869767 GAGCAGGATATTGTTGCGGAG 59.130 52.381 0.00 0.00 42.47 4.63
712 800 2.434336 AGCAGGATATTGTTGCGGAGTA 59.566 45.455 0.00 0.00 42.47 2.59
714 802 3.815401 GCAGGATATTGTTGCGGAGTATT 59.185 43.478 0.00 0.00 0.00 1.89
715 803 4.275936 GCAGGATATTGTTGCGGAGTATTT 59.724 41.667 0.00 0.00 0.00 1.40
716 804 5.221048 GCAGGATATTGTTGCGGAGTATTTT 60.221 40.000 0.00 0.00 0.00 1.82
717 805 6.201517 CAGGATATTGTTGCGGAGTATTTTG 58.798 40.000 0.00 0.00 0.00 2.44
718 806 4.976116 GGATATTGTTGCGGAGTATTTTGC 59.024 41.667 0.00 0.00 0.00 3.68
845 946 2.118404 CCACACCACACCACACCAC 61.118 63.158 0.00 0.00 0.00 4.16
846 947 1.377856 CACACCACACCACACCACA 60.378 57.895 0.00 0.00 0.00 4.17
848 949 2.118404 CACCACACCACACCACACC 61.118 63.158 0.00 0.00 0.00 4.16
849 950 2.273776 CCACACCACACCACACCA 59.726 61.111 0.00 0.00 0.00 4.17
850 951 1.152777 CCACACCACACCACACCAT 60.153 57.895 0.00 0.00 0.00 3.55
851 952 1.454572 CCACACCACACCACACCATG 61.455 60.000 0.00 0.00 0.00 3.66
853 954 1.827354 CACCACACCACACCATGCA 60.827 57.895 0.00 0.00 0.00 3.96
873 975 2.613595 CACCTCTCTCTCTCTCACATCG 59.386 54.545 0.00 0.00 0.00 3.84
895 997 3.295973 CCTTCCTTTTTGTTCTCCACCA 58.704 45.455 0.00 0.00 0.00 4.17
918 1020 7.717436 ACCACCTCTCTCTTTTCTTTTCTTTAG 59.283 37.037 0.00 0.00 0.00 1.85
919 1021 7.717436 CCACCTCTCTCTTTTCTTTTCTTTAGT 59.283 37.037 0.00 0.00 0.00 2.24
920 1022 8.555361 CACCTCTCTCTTTTCTTTTCTTTAGTG 58.445 37.037 0.00 0.00 0.00 2.74
921 1023 8.268605 ACCTCTCTCTTTTCTTTTCTTTAGTGT 58.731 33.333 0.00 0.00 0.00 3.55
936 1038 0.389391 AGTGTGTGTTGAGAGTCCCG 59.611 55.000 0.00 0.00 0.00 5.14
1042 1146 1.277557 AGAGAAGGCGAACAGAAGCAT 59.722 47.619 0.00 0.00 34.54 3.79
1043 1147 1.663135 GAGAAGGCGAACAGAAGCATC 59.337 52.381 0.00 0.00 34.54 3.91
1044 1148 1.002430 AGAAGGCGAACAGAAGCATCA 59.998 47.619 0.00 0.00 34.54 3.07
1045 1149 1.396301 GAAGGCGAACAGAAGCATCAG 59.604 52.381 0.00 0.00 34.54 2.90
1046 1150 1.023513 AGGCGAACAGAAGCATCAGC 61.024 55.000 0.00 0.00 42.56 4.26
1140 1247 1.160329 GCGAGTTCCCGATCCCAATG 61.160 60.000 0.00 0.00 0.00 2.82
1141 1248 1.160329 CGAGTTCCCGATCCCAATGC 61.160 60.000 0.00 0.00 0.00 3.56
1142 1249 0.107214 GAGTTCCCGATCCCAATGCA 60.107 55.000 0.00 0.00 0.00 3.96
1143 1250 0.552848 AGTTCCCGATCCCAATGCAT 59.447 50.000 0.00 0.00 0.00 3.96
1144 1251 0.954452 GTTCCCGATCCCAATGCATC 59.046 55.000 0.00 0.00 0.00 3.91
1145 1252 0.550432 TTCCCGATCCCAATGCATCA 59.450 50.000 0.00 0.00 0.00 3.07
1224 1331 3.446570 GCCATGGAGCTGCACCAC 61.447 66.667 21.00 5.24 40.36 4.16
1245 1352 2.897846 CACGCCAACCACAACGGA 60.898 61.111 0.00 0.00 38.63 4.69
2208 2327 1.081108 GCTCAAGCTCGACTGACGT 60.081 57.895 0.00 0.00 43.13 4.34
2229 2358 0.178990 ACAAAGAAGCCCTGGTGTCC 60.179 55.000 0.00 0.00 0.00 4.02
2304 2433 4.695217 TTAATTTCACTGTTCCATCGGC 57.305 40.909 0.00 0.00 0.00 5.54
2338 2467 5.644644 GAAGCAGAGAGAAGAGAAGAGAAG 58.355 45.833 0.00 0.00 0.00 2.85
2339 2468 4.922206 AGCAGAGAGAAGAGAAGAGAAGA 58.078 43.478 0.00 0.00 0.00 2.87
2340 2469 4.946157 AGCAGAGAGAAGAGAAGAGAAGAG 59.054 45.833 0.00 0.00 0.00 2.85
2341 2470 4.943705 GCAGAGAGAAGAGAAGAGAAGAGA 59.056 45.833 0.00 0.00 0.00 3.10
2342 2471 5.415701 GCAGAGAGAAGAGAAGAGAAGAGAA 59.584 44.000 0.00 0.00 0.00 2.87
2343 2472 6.623767 GCAGAGAGAAGAGAAGAGAAGAGAAC 60.624 46.154 0.00 0.00 0.00 3.01
2344 2473 5.946377 AGAGAGAAGAGAAGAGAAGAGAACC 59.054 44.000 0.00 0.00 0.00 3.62
2364 2493 3.628942 ACCAAAAACAAACCCGAGTCTAC 59.371 43.478 0.00 0.00 0.00 2.59
2379 2508 5.453903 CCGAGTCTACCATCATCTCCATTTT 60.454 44.000 0.00 0.00 0.00 1.82
2493 2625 7.404671 TCAATTTATTTTTCCTGGACCTAGC 57.595 36.000 0.00 0.00 0.00 3.42
2576 2719 1.538512 TGAGCTGAGCATTTGAGTTGC 59.461 47.619 7.39 0.00 40.45 4.17
2593 2736 3.394940 AGTTGCCATGGATCAGATCAGAT 59.605 43.478 18.40 0.00 0.00 2.90
2594 2737 3.418684 TGCCATGGATCAGATCAGATG 57.581 47.619 18.40 12.32 0.00 2.90
2596 2739 3.587506 TGCCATGGATCAGATCAGATGAT 59.412 43.478 18.40 0.21 40.08 2.45
2615 2758 6.711194 AGATGATCAGAGGCTGTATGAAATTG 59.289 38.462 0.09 0.00 32.61 2.32
2641 2784 6.539649 TCTGACTTGTTTACAATTTCTCCG 57.460 37.500 0.00 0.00 35.02 4.63
2652 2795 9.887406 GTTTACAATTTCTCCGTTTATCTTCAA 57.113 29.630 0.00 0.00 0.00 2.69
2657 2800 9.846248 CAATTTCTCCGTTTATCTTCAATTTCT 57.154 29.630 0.00 0.00 0.00 2.52
2659 2802 7.611213 TTCTCCGTTTATCTTCAATTTCTCC 57.389 36.000 0.00 0.00 0.00 3.71
2660 2803 6.707290 TCTCCGTTTATCTTCAATTTCTCCA 58.293 36.000 0.00 0.00 0.00 3.86
2661 2804 7.338710 TCTCCGTTTATCTTCAATTTCTCCAT 58.661 34.615 0.00 0.00 0.00 3.41
2662 2805 7.829211 TCTCCGTTTATCTTCAATTTCTCCATT 59.171 33.333 0.00 0.00 0.00 3.16
2682 2825 6.099413 TCCATTCTAATCTGCAGAGTCTGAAT 59.901 38.462 25.86 25.86 32.44 2.57
2683 2826 6.766944 CCATTCTAATCTGCAGAGTCTGAATT 59.233 38.462 27.54 19.08 32.44 2.17
2684 2827 7.282675 CCATTCTAATCTGCAGAGTCTGAATTT 59.717 37.037 27.54 16.87 32.44 1.82
2685 2828 7.840342 TTCTAATCTGCAGAGTCTGAATTTC 57.160 36.000 21.62 6.05 32.44 2.17
2686 2829 7.180322 TCTAATCTGCAGAGTCTGAATTTCT 57.820 36.000 21.62 5.44 32.44 2.52
2687 2830 7.619050 TCTAATCTGCAGAGTCTGAATTTCTT 58.381 34.615 21.62 7.94 32.44 2.52
2688 2831 8.099537 TCTAATCTGCAGAGTCTGAATTTCTTT 58.900 33.333 21.62 7.73 32.44 2.52
2689 2832 7.521871 AATCTGCAGAGTCTGAATTTCTTTT 57.478 32.000 24.55 3.06 32.44 2.27
2699 2842 8.455903 AGTCTGAATTTCTTTTGAGAACATGA 57.544 30.769 0.00 0.00 0.00 3.07
2782 2925 0.742505 TGCATGCTTAATCTGCAGCC 59.257 50.000 20.33 0.00 44.04 4.85
2882 3025 0.813610 TTCACCACTCACAAGCCACG 60.814 55.000 0.00 0.00 0.00 4.94
2888 3031 0.597637 ACTCACAAGCCACGAAGACG 60.598 55.000 0.00 0.00 45.75 4.18
2899 3049 2.481449 CCACGAAGACGATAGAAAGGGG 60.481 54.545 0.00 0.00 42.66 4.79
2908 3058 4.810345 ACGATAGAAAGGGGAGAGAGATT 58.190 43.478 0.00 0.00 41.38 2.40
2929 3079 3.157087 TCTTGTCAAGAATTTGGGAGCC 58.843 45.455 13.00 0.00 33.83 4.70
2930 3080 2.978156 TGTCAAGAATTTGGGAGCCT 57.022 45.000 0.00 0.00 34.97 4.58
2943 3093 1.067250 GAGCCTGAGAGCGATGGAC 59.933 63.158 0.00 0.00 38.01 4.02
2968 3119 5.121611 CGGAGGGTGAAAATTAAAATTTGGC 59.878 40.000 1.61 0.00 38.53 4.52
2969 3120 5.414454 GGAGGGTGAAAATTAAAATTTGGCC 59.586 40.000 0.00 0.00 38.53 5.36
2983 3134 3.703127 GGCCGTCCCCGTTTCTCT 61.703 66.667 0.00 0.00 0.00 3.10
2990 3141 2.640184 GTCCCCGTTTCTCTATTTGGG 58.360 52.381 0.00 0.00 36.37 4.12
2993 3144 1.014352 CCGTTTCTCTATTTGGGGCG 58.986 55.000 0.00 0.00 0.00 6.13
3006 3157 0.832135 TGGGGCGGATGATAGTCCTC 60.832 60.000 0.00 0.00 36.07 3.71
3070 3226 2.800629 CGCAATCAATCATTCTTGGGGC 60.801 50.000 0.00 0.00 0.00 5.80
3202 3358 1.304282 TGCTCCTGCAGGGGATTTC 59.696 57.895 37.54 18.85 45.31 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.533753 TTTCCCAAAGGCAGCCAGG 60.534 57.895 15.80 12.38 0.00 4.45
1 2 1.969862 CTTTCCCAAAGGCAGCCAG 59.030 57.895 15.80 2.56 34.85 4.85
19 20 1.156566 CTAGGGTCTAGGGCCTCCC 59.843 68.421 18.99 18.99 45.90 4.30
20 21 0.178955 GTCTAGGGTCTAGGGCCTCC 60.179 65.000 10.74 4.96 0.00 4.30
21 22 0.537828 CGTCTAGGGTCTAGGGCCTC 60.538 65.000 10.74 0.00 0.00 4.70
133 136 3.317430 AGCAAGAAGAGACCAAAAGCAAG 59.683 43.478 0.00 0.00 0.00 4.01
156 159 4.741239 GGGAGGGGAGGGTGAGCA 62.741 72.222 0.00 0.00 0.00 4.26
158 161 3.700350 AGGGGAGGGGAGGGTGAG 61.700 72.222 0.00 0.00 0.00 3.51
159 162 3.695825 GAGGGGAGGGGAGGGTGA 61.696 72.222 0.00 0.00 0.00 4.02
160 163 4.825679 GGAGGGGAGGGGAGGGTG 62.826 77.778 0.00 0.00 0.00 4.61
164 167 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
185 188 0.478507 GGAGGAGGAGGAGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
233 243 4.279420 AGCTTCCTTCATGGACAGTTTTTC 59.721 41.667 0.00 0.00 46.14 2.29
234 244 4.218312 AGCTTCCTTCATGGACAGTTTTT 58.782 39.130 0.00 0.00 46.14 1.94
290 347 1.542547 CCACACACCACCAAGGACTAC 60.543 57.143 0.00 0.00 41.22 2.73
331 388 1.905894 AGCCTTCCTTTGACCTCTCTC 59.094 52.381 0.00 0.00 0.00 3.20
332 389 1.627834 CAGCCTTCCTTTGACCTCTCT 59.372 52.381 0.00 0.00 0.00 3.10
408 478 4.575645 AGTACTAGTAGTAGGAAGCAAGCG 59.424 45.833 10.38 0.00 30.12 4.68
467 551 0.531200 CGAGTGAGGGGTTACTCCAC 59.469 60.000 3.28 0.00 40.07 4.02
468 552 1.255667 GCGAGTGAGGGGTTACTCCA 61.256 60.000 3.28 0.00 40.07 3.86
469 553 0.971447 AGCGAGTGAGGGGTTACTCC 60.971 60.000 0.00 0.00 40.07 3.85
489 577 3.782244 AAGCAAAGCGAGCGAGCG 61.782 61.111 0.00 0.00 43.00 5.03
490 578 2.202272 CAAGCAAAGCGAGCGAGC 60.202 61.111 0.00 0.00 37.01 5.03
491 579 2.202272 GCAAGCAAAGCGAGCGAG 60.202 61.111 0.00 0.00 37.01 5.03
492 580 3.726517 GGCAAGCAAAGCGAGCGA 61.727 61.111 0.00 0.00 34.96 4.93
493 581 3.541093 TTGGCAAGCAAAGCGAGCG 62.541 57.895 0.00 0.00 34.96 5.03
494 582 1.731969 CTTGGCAAGCAAAGCGAGC 60.732 57.895 15.25 0.00 33.81 5.03
495 583 0.311790 TTCTTGGCAAGCAAAGCGAG 59.688 50.000 22.31 0.00 0.00 5.03
496 584 0.030638 GTTCTTGGCAAGCAAAGCGA 59.969 50.000 22.31 0.34 0.00 4.93
497 585 0.248990 TGTTCTTGGCAAGCAAAGCG 60.249 50.000 22.31 0.00 0.00 4.68
498 586 1.494824 CTGTTCTTGGCAAGCAAAGC 58.505 50.000 22.31 8.23 0.00 3.51
499 587 1.494824 GCTGTTCTTGGCAAGCAAAG 58.505 50.000 22.31 16.96 0.00 2.77
500 588 0.104671 GGCTGTTCTTGGCAAGCAAA 59.895 50.000 22.31 9.73 0.00 3.68
545 633 1.561542 GATGCAGGAAGGAAGGAAGGA 59.438 52.381 0.00 0.00 0.00 3.36
548 636 2.376518 ACAAGATGCAGGAAGGAAGGAA 59.623 45.455 0.00 0.00 0.00 3.36
567 655 1.301401 GCTGTACTCACCCGCAACA 60.301 57.895 0.00 0.00 0.00 3.33
574 662 0.175989 GGGTAGCTGCTGTACTCACC 59.824 60.000 13.43 10.43 0.00 4.02
598 686 4.450053 CAAAGGAGGAGATCAGCTTTAGG 58.550 47.826 0.00 0.00 0.00 2.69
607 695 7.053498 AGAAGATAAAAGCAAAGGAGGAGATC 58.947 38.462 0.00 0.00 0.00 2.75
608 696 6.967897 AGAAGATAAAAGCAAAGGAGGAGAT 58.032 36.000 0.00 0.00 0.00 2.75
611 699 8.552296 AGATTAGAAGATAAAAGCAAAGGAGGA 58.448 33.333 0.00 0.00 0.00 3.71
614 702 9.520515 ACAAGATTAGAAGATAAAAGCAAAGGA 57.479 29.630 0.00 0.00 0.00 3.36
618 706 9.410556 GCAAACAAGATTAGAAGATAAAAGCAA 57.589 29.630 0.00 0.00 0.00 3.91
619 707 8.575589 TGCAAACAAGATTAGAAGATAAAAGCA 58.424 29.630 0.00 0.00 0.00 3.91
620 708 8.970691 TGCAAACAAGATTAGAAGATAAAAGC 57.029 30.769 0.00 0.00 0.00 3.51
624 712 7.416664 GCCCATGCAAACAAGATTAGAAGATAA 60.417 37.037 0.00 0.00 37.47 1.75
625 713 6.039717 GCCCATGCAAACAAGATTAGAAGATA 59.960 38.462 0.00 0.00 37.47 1.98
626 714 5.163478 GCCCATGCAAACAAGATTAGAAGAT 60.163 40.000 0.00 0.00 37.47 2.40
706 794 8.707839 ACAAACAAATAAATGCAAAATACTCCG 58.292 29.630 0.00 0.00 0.00 4.63
845 946 1.136695 GAGAGAGAGAGGTGCATGGTG 59.863 57.143 0.00 0.00 0.00 4.17
846 947 1.006998 AGAGAGAGAGAGGTGCATGGT 59.993 52.381 0.00 0.00 0.00 3.55
848 949 2.099592 GTGAGAGAGAGAGAGGTGCATG 59.900 54.545 0.00 0.00 0.00 4.06
849 950 2.291475 TGTGAGAGAGAGAGAGGTGCAT 60.291 50.000 0.00 0.00 0.00 3.96
850 951 1.074566 TGTGAGAGAGAGAGAGGTGCA 59.925 52.381 0.00 0.00 0.00 4.57
851 952 1.832883 TGTGAGAGAGAGAGAGGTGC 58.167 55.000 0.00 0.00 0.00 5.01
853 954 2.917933 CGATGTGAGAGAGAGAGAGGT 58.082 52.381 0.00 0.00 0.00 3.85
873 975 2.035961 GGTGGAGAACAAAAAGGAAGGC 59.964 50.000 0.00 0.00 0.00 4.35
895 997 8.268605 ACACTAAAGAAAAGAAAAGAGAGAGGT 58.731 33.333 0.00 0.00 0.00 3.85
918 1020 0.387929 TCGGGACTCTCAACACACAC 59.612 55.000 0.00 0.00 0.00 3.82
919 1021 0.673985 CTCGGGACTCTCAACACACA 59.326 55.000 0.00 0.00 0.00 3.72
920 1022 0.959553 TCTCGGGACTCTCAACACAC 59.040 55.000 0.00 0.00 0.00 3.82
921 1023 1.699730 TTCTCGGGACTCTCAACACA 58.300 50.000 0.00 0.00 0.00 3.72
936 1038 4.207019 CGCCAACAAAATTCAGTGTTTCTC 59.793 41.667 0.00 0.00 35.81 2.87
1042 1146 4.303993 TGACGCTGCTGCTGCTGA 62.304 61.111 25.43 9.33 40.01 4.26
1043 1147 3.789858 CTGACGCTGCTGCTGCTG 61.790 66.667 25.43 20.66 40.48 4.41
1094 1201 2.570135 GCACAGAAAGATCCATCCTCC 58.430 52.381 0.00 0.00 0.00 4.30
1224 1331 2.897846 TTGTGGTTGGCGTGGTCG 60.898 61.111 0.00 0.00 40.37 4.79
1278 1391 3.305516 TCCTCAGACGCAGCAGCA 61.306 61.111 0.82 0.00 42.27 4.41
1286 1399 2.487428 CGGAGCTGTCCTCAGACG 59.513 66.667 0.00 0.00 46.74 4.18
1542 1655 3.282157 TAGCCGTAGCCGTAGCCG 61.282 66.667 0.00 0.00 41.25 5.52
1543 1656 2.334295 GTAGCCGTAGCCGTAGCC 59.666 66.667 0.00 0.00 41.25 3.93
1544 1657 2.051525 CGTAGCCGTAGCCGTAGC 60.052 66.667 0.00 0.00 41.25 3.58
1545 1658 2.635899 CCGTAGCCGTAGCCGTAG 59.364 66.667 0.00 0.00 41.25 3.51
1546 1659 3.585990 GCCGTAGCCGTAGCCGTA 61.586 66.667 0.00 0.00 41.25 4.02
2208 2327 0.550914 ACACCAGGGCTTCTTTGTGA 59.449 50.000 0.00 0.00 32.75 3.58
2243 2372 0.654683 GCTAGCAGAATCAGCAACCG 59.345 55.000 10.63 0.00 35.35 4.44
2338 2467 3.129813 ACTCGGGTTTGTTTTTGGTTCTC 59.870 43.478 0.00 0.00 0.00 2.87
2339 2468 3.093814 ACTCGGGTTTGTTTTTGGTTCT 58.906 40.909 0.00 0.00 0.00 3.01
2340 2469 3.129813 AGACTCGGGTTTGTTTTTGGTTC 59.870 43.478 0.00 0.00 0.00 3.62
2341 2470 3.093814 AGACTCGGGTTTGTTTTTGGTT 58.906 40.909 0.00 0.00 0.00 3.67
2342 2471 2.730382 AGACTCGGGTTTGTTTTTGGT 58.270 42.857 0.00 0.00 0.00 3.67
2343 2472 3.004002 GGTAGACTCGGGTTTGTTTTTGG 59.996 47.826 0.00 0.00 0.00 3.28
2344 2473 3.628487 TGGTAGACTCGGGTTTGTTTTTG 59.372 43.478 0.00 0.00 0.00 2.44
2379 2508 6.801575 ACAAGATAAACAGCGAAAGGAAAAA 58.198 32.000 0.00 0.00 0.00 1.94
2501 2633 3.669251 ACCAAGGAGACGAAGAAGAAG 57.331 47.619 0.00 0.00 0.00 2.85
2503 2635 2.037251 CCAACCAAGGAGACGAAGAAGA 59.963 50.000 0.00 0.00 0.00 2.87
2593 2736 5.993055 TCAATTTCATACAGCCTCTGATCA 58.007 37.500 0.00 0.00 35.18 2.92
2594 2737 7.444792 AGAATCAATTTCATACAGCCTCTGATC 59.555 37.037 0.29 0.00 36.75 2.92
2596 2739 6.541278 CAGAATCAATTTCATACAGCCTCTGA 59.459 38.462 0.29 0.00 36.75 3.27
2603 2746 9.903682 AAACAAGTCAGAATCAATTTCATACAG 57.096 29.630 0.00 0.00 36.75 2.74
2615 2758 7.746475 CGGAGAAATTGTAAACAAGTCAGAATC 59.254 37.037 1.62 0.00 39.47 2.52
2652 2795 6.897986 ACTCTGCAGATTAGAATGGAGAAAT 58.102 36.000 18.63 0.00 42.35 2.17
2657 2800 4.958581 TCAGACTCTGCAGATTAGAATGGA 59.041 41.667 18.63 4.58 0.00 3.41
2658 2801 5.273674 TCAGACTCTGCAGATTAGAATGG 57.726 43.478 18.63 5.27 0.00 3.16
2659 2802 7.789273 AATTCAGACTCTGCAGATTAGAATG 57.211 36.000 23.27 15.24 0.00 2.67
2660 2803 8.266473 AGAAATTCAGACTCTGCAGATTAGAAT 58.734 33.333 18.63 19.39 0.00 2.40
2661 2804 7.619050 AGAAATTCAGACTCTGCAGATTAGAA 58.381 34.615 18.63 18.11 0.00 2.10
2662 2805 7.180322 AGAAATTCAGACTCTGCAGATTAGA 57.820 36.000 18.63 10.47 0.00 2.10
2682 2825 6.638096 TGCATCTCATGTTCTCAAAAGAAA 57.362 33.333 0.00 0.00 43.04 2.52
2683 2826 6.638096 TTGCATCTCATGTTCTCAAAAGAA 57.362 33.333 0.00 0.00 39.22 2.52
2684 2827 6.657966 AGATTGCATCTCATGTTCTCAAAAGA 59.342 34.615 0.00 0.00 33.42 2.52
2685 2828 6.853720 AGATTGCATCTCATGTTCTCAAAAG 58.146 36.000 0.00 0.00 33.42 2.27
2686 2829 6.829229 AGATTGCATCTCATGTTCTCAAAA 57.171 33.333 0.00 0.00 33.42 2.44
2699 2842 1.138568 CCCAGGGAGAGATTGCATCT 58.861 55.000 0.00 0.00 43.70 2.90
2715 2858 2.354704 CGCCTGAAAGATACAAGACCCA 60.355 50.000 0.00 0.00 34.07 4.51
2716 2859 2.280628 CGCCTGAAAGATACAAGACCC 58.719 52.381 0.00 0.00 34.07 4.46
2782 2925 0.670546 CAGTAACAGCACCGACAGGG 60.671 60.000 0.00 0.00 43.47 4.45
2831 2974 1.627329 GGATCAGATCAGGCATAGGCA 59.373 52.381 12.66 0.00 43.71 4.75
2882 3025 4.208746 TCTCTCCCCTTTCTATCGTCTTC 58.791 47.826 0.00 0.00 0.00 2.87
2888 3031 6.326323 ACAAGAATCTCTCTCCCCTTTCTATC 59.674 42.308 0.00 0.00 31.02 2.08
2908 3058 3.157087 GGCTCCCAAATTCTTGACAAGA 58.843 45.455 13.99 13.99 34.14 3.02
2922 3072 2.042537 ATCGCTCTCAGGCTCCCA 60.043 61.111 0.00 0.00 0.00 4.37
2929 3079 2.069465 CTCCGGTCCATCGCTCTCAG 62.069 65.000 0.00 0.00 0.00 3.35
2930 3080 2.044352 TCCGGTCCATCGCTCTCA 60.044 61.111 0.00 0.00 0.00 3.27
2943 3093 5.641636 CCAAATTTTAATTTTCACCCTCCGG 59.358 40.000 0.00 0.00 36.52 5.14
2983 3134 2.304761 GGACTATCATCCGCCCCAAATA 59.695 50.000 0.00 0.00 0.00 1.40
2990 3141 1.587054 CCGAGGACTATCATCCGCC 59.413 63.158 0.00 0.00 44.22 6.13
2993 3144 0.605589 CAGGCCGAGGACTATCATCC 59.394 60.000 0.00 0.00 39.28 3.51
3049 3201 2.800629 GCCCCAAGAATGATTGATTGCG 60.801 50.000 0.00 0.00 31.55 4.85


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

AutoCloner maintained by Alex Coulton.