Multiple sequence alignment - TraesCS7D01G534800

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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 TraesCS7D01G534800 chr7D 100.000 3052 0 0 1 3052 627218332 627221383 0.000000e+00 5637.0
1 TraesCS7D01G534800 chr7D 81.354 960 155 10 1042 1979 627227190 627228147 0.000000e+00 760.0
2 TraesCS7D01G534800 chr7D 80.971 762 125 6 1004 1746 627169514 627170274 1.220000e-163 586.0
3 TraesCS7D01G534800 chr7D 94.146 205 10 2 2788 2992 627218878 627219080 8.220000e-81 311.0
4 TraesCS7D01G534800 chr7D 94.146 205 10 2 547 749 627221119 627221323 8.220000e-81 311.0
5 TraesCS7D01G534800 chr7D 95.000 60 2 1 757 815 627219033 627219092 3.240000e-15 93.5
6 TraesCS7D01G534800 chr7D 95.000 60 2 1 702 761 627219088 627219146 3.240000e-15 93.5
7 TraesCS7D01G534800 chr7D 95.833 48 1 1 2945 2992 627219088 627219134 3.260000e-10 76.8
8 TraesCS7D01G534800 chr7D 95.833 48 1 1 757 803 627221276 627221323 3.260000e-10 76.8
9 TraesCS7D01G534800 chr7A 91.770 2017 119 26 1 2008 722776835 722778813 0.000000e+00 2761.0
10 TraesCS7D01G534800 chr7A 80.294 954 155 20 1043 1975 722763920 722764861 0.000000e+00 689.0
11 TraesCS7D01G534800 chr7A 91.328 369 25 3 2669 3036 722779452 722779814 5.880000e-137 497.0
12 TraesCS7D01G534800 chr7A 91.220 205 15 3 2788 2992 722777347 722777548 3.000000e-70 276.0
13 TraesCS7D01G534800 chr7A 90.686 204 13 5 547 749 722779572 722779770 1.800000e-67 267.0
14 TraesCS7D01G534800 chr7A 93.333 60 3 1 702 761 722777556 722777614 1.510000e-13 87.9
15 TraesCS7D01G534800 chr7A 93.750 48 2 1 2945 2992 722777556 722777602 1.520000e-08 71.3
16 TraesCS7D01G534800 chr7B 92.221 1324 82 2 705 2008 727862924 727864246 0.000000e+00 1855.0
17 TraesCS7D01G534800 chr7B 90.338 828 65 12 772 1588 727439120 727438297 0.000000e+00 1072.0
18 TraesCS7D01G534800 chr7B 90.139 791 56 7 1580 2367 727437186 727436415 0.000000e+00 1009.0
19 TraesCS7D01G534800 chr7B 88.794 821 76 10 1 815 727862169 727862979 0.000000e+00 992.0
20 TraesCS7D01G534800 chr7B 87.206 766 60 17 1 761 727423738 727423006 0.000000e+00 837.0
21 TraesCS7D01G534800 chr7B 80.858 956 149 20 1043 1975 727608283 727607339 0.000000e+00 721.0
22 TraesCS7D01G534800 chr7B 91.757 461 35 2 2593 3052 727865311 727865769 3.320000e-179 638.0
23 TraesCS7D01G534800 chr7B 86.831 486 51 9 284 761 727439557 727439077 5.790000e-147 531.0
24 TraesCS7D01G534800 chr7B 87.847 288 32 2 1 286 727439958 727439672 4.880000e-88 335.0
25 TraesCS7D01G534800 chr7B 93.171 205 11 3 2788 2992 727423219 727423018 6.400000e-77 298.0
26 TraesCS7D01G534800 chr7B 93.989 183 10 1 760 941 727423062 727422880 3.000000e-70 276.0
27 TraesCS7D01G534800 chr7B 91.542 201 15 2 547 746 727865507 727865706 3.000000e-70 276.0
28 TraesCS7D01G534800 chr7B 89.529 191 13 2 2802 2992 727862730 727862913 5.090000e-58 235.0
29 TraesCS7D01G534800 chr7B 86.634 202 20 4 2794 2992 727439286 727439089 1.840000e-52 217.0
30 TraesCS7D01G534800 chr7B 90.152 132 12 1 2501 2632 727436206 727436076 1.460000e-38 171.0
31 TraesCS7D01G534800 chr7B 87.050 139 10 6 2130 2263 727864266 727864401 1.900000e-32 150.0
32 TraesCS7D01G534800 chr7B 86.957 115 5 2 2263 2367 727864673 727864787 1.490000e-23 121.0
33 TraesCS7D01G534800 chr7B 93.333 60 3 1 757 815 727862866 727862925 1.510000e-13 87.9
34 TraesCS7D01G534800 chr7B 95.556 45 1 1 2948 2992 727862924 727862967 1.520000e-08 71.3
35 TraesCS7D01G534800 chr7B 93.333 45 2 1 757 800 727865662 727865706 7.060000e-07 65.8
36 TraesCS7D01G534800 chr7B 100.000 32 0 0 2459 2490 727864925 727864956 3.290000e-05 60.2
37 TraesCS7D01G534800 chr2B 74.550 888 195 24 1108 1975 796341340 796342216 2.890000e-95 359.0
38 TraesCS7D01G534800 chr2A 81.343 134 23 2 1108 1240 761542613 761542481 1.160000e-19 108.0


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 TraesCS7D01G534800 chr7D 627218332 627221383 3051 False 942.800000 5637 95.708286 1 3052 7 chr7D.!!$F3 3051
1 TraesCS7D01G534800 chr7D 627227190 627228147 957 False 760.000000 760 81.354000 1042 1979 1 chr7D.!!$F2 937
2 TraesCS7D01G534800 chr7D 627169514 627170274 760 False 586.000000 586 80.971000 1004 1746 1 chr7D.!!$F1 742
3 TraesCS7D01G534800 chr7A 722763920 722764861 941 False 689.000000 689 80.294000 1043 1975 1 chr7A.!!$F1 932
4 TraesCS7D01G534800 chr7A 722776835 722779814 2979 False 660.033333 2761 92.014500 1 3036 6 chr7A.!!$F2 3035
5 TraesCS7D01G534800 chr7B 727607339 727608283 944 True 721.000000 721 80.858000 1043 1975 1 chr7B.!!$R1 932
6 TraesCS7D01G534800 chr7B 727436076 727439958 3882 True 555.833333 1072 88.656833 1 2992 6 chr7B.!!$R3 2991
7 TraesCS7D01G534800 chr7B 727422880 727423738 858 True 470.333333 837 91.455333 1 2992 3 chr7B.!!$R2 2991
8 TraesCS7D01G534800 chr7B 727862169 727865769 3600 False 413.836364 1855 91.824727 1 3052 11 chr7B.!!$F1 3051
9 TraesCS7D01G534800 chr2B 796341340 796342216 876 False 359.000000 359 74.550000 1108 1975 1 chr2B.!!$F1 867

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
952 1230 0.108396 TGCCTAGTTCTTGCAGCACA 59.892 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 3657 0.247655 CAATGGTGTGTGTATCGCGC 60.248 55.0 0.0 0.0 36.46 6.86 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
100 113 5.716094 ACAAAACTATTGCCGGTTATTTCC 58.284 37.500 1.90 0.00 0.00 3.13
105 118 0.882474 TTGCCGGTTATTTCCCAACG 59.118 50.000 1.90 0.00 0.00 4.10
222 236 8.546244 CAGAAACTGTATTACATACATGAGCAG 58.454 37.037 0.00 0.00 44.11 4.24
243 257 9.294030 GAGCAGTTATTCACATATTTTGAAAGG 57.706 33.333 1.51 0.00 36.57 3.11
273 287 5.407407 ACTTACACATCTTAGTGACCCTG 57.593 43.478 0.57 0.00 42.05 4.45
303 434 4.388485 TGTACATATTAGCACATGGCCTG 58.612 43.478 3.32 2.01 46.50 4.85
317 448 1.244816 GGCCTGTGTAACTTCCCAAC 58.755 55.000 0.00 0.00 38.04 3.77
335 466 3.399330 CAACGAGGAAGCCTAACAAGAA 58.601 45.455 0.00 0.00 31.76 2.52
338 469 4.003648 ACGAGGAAGCCTAACAAGAAATG 58.996 43.478 0.00 0.00 31.76 2.32
393 524 7.034397 AGCGATAACAACCTAGACTAAAGTTC 58.966 38.462 0.00 0.00 0.00 3.01
435 567 3.111939 CTCGACTAGCTCACCCCG 58.888 66.667 0.00 0.00 0.00 5.73
443 575 2.289506 ACTAGCTCACCCCGAAAAAGAC 60.290 50.000 0.00 0.00 0.00 3.01
447 579 2.935676 GCTCACCCCGAAAAAGACTAGG 60.936 54.545 0.00 0.00 0.00 3.02
449 581 2.301009 TCACCCCGAAAAAGACTAGGTC 59.699 50.000 0.00 0.00 0.00 3.85
450 582 2.038033 CACCCCGAAAAAGACTAGGTCA 59.962 50.000 0.00 0.00 34.60 4.02
455 587 4.928020 CCCGAAAAAGACTAGGTCAACTAC 59.072 45.833 0.00 0.00 34.60 2.73
523 684 2.995939 GAGATGTTGCAATGTGTCTCGA 59.004 45.455 0.59 0.00 0.00 4.04
535 696 2.227194 GTGTCTCGAATTGGGGTGTTT 58.773 47.619 0.00 0.00 0.00 2.83
540 701 5.221682 TGTCTCGAATTGGGGTGTTTACTTA 60.222 40.000 0.00 0.00 0.00 2.24
541 702 5.121298 GTCTCGAATTGGGGTGTTTACTTAC 59.879 44.000 0.00 0.00 0.00 2.34
549 711 5.131784 TGGGGTGTTTACTTACGTGAAAAT 58.868 37.500 0.00 0.00 0.00 1.82
576 741 9.953565 AGTATACAATTTTCTTTACTAGGCACA 57.046 29.630 5.50 0.00 0.00 4.57
595 760 8.443953 AGGCACATAGACAATTAGAGAAATTC 57.556 34.615 0.00 0.00 35.54 2.17
612 777 8.713271 AGAGAAATTCGACTAAAATTCAGACAC 58.287 33.333 0.00 0.00 0.00 3.67
670 837 3.146847 GGGTAACACTTTGCTAGCAACT 58.853 45.455 29.33 14.78 34.82 3.16
730 898 8.867112 TTGTTTCTTGGCTATAGATAGTAACG 57.133 34.615 3.21 0.00 32.96 3.18
731 899 8.229253 TGTTTCTTGGCTATAGATAGTAACGA 57.771 34.615 3.21 0.00 32.96 3.85
732 900 8.350722 TGTTTCTTGGCTATAGATAGTAACGAG 58.649 37.037 3.21 0.61 32.96 4.18
733 901 7.450124 TTCTTGGCTATAGATAGTAACGAGG 57.550 40.000 3.21 0.00 32.96 4.63
734 902 6.540995 TCTTGGCTATAGATAGTAACGAGGT 58.459 40.000 3.21 0.00 32.96 3.85
735 903 7.683578 TCTTGGCTATAGATAGTAACGAGGTA 58.316 38.462 3.21 0.00 32.96 3.08
736 904 8.159447 TCTTGGCTATAGATAGTAACGAGGTAA 58.841 37.037 3.21 0.00 32.96 2.85
737 905 7.678947 TGGCTATAGATAGTAACGAGGTAAC 57.321 40.000 3.21 0.00 32.96 2.50
738 906 7.456725 TGGCTATAGATAGTAACGAGGTAACT 58.543 38.462 3.21 0.00 40.62 2.24
739 907 7.389884 TGGCTATAGATAGTAACGAGGTAACTG 59.610 40.741 3.21 0.00 38.94 3.16
740 908 7.390162 GGCTATAGATAGTAACGAGGTAACTGT 59.610 40.741 3.21 0.00 38.94 3.55
741 909 9.429359 GCTATAGATAGTAACGAGGTAACTGTA 57.571 37.037 3.21 0.00 38.94 2.74
753 921 2.870411 GGTAACTGTATTCCATGGACGC 59.130 50.000 15.91 8.18 0.00 5.19
754 922 2.038387 AACTGTATTCCATGGACGCC 57.962 50.000 15.91 5.32 0.00 5.68
755 923 0.179084 ACTGTATTCCATGGACGCCG 60.179 55.000 15.91 6.60 0.00 6.46
756 924 0.179084 CTGTATTCCATGGACGCCGT 60.179 55.000 15.91 0.00 0.00 5.68
757 925 1.067974 CTGTATTCCATGGACGCCGTA 59.932 52.381 15.91 0.00 0.00 4.02
758 926 1.202440 TGTATTCCATGGACGCCGTAC 60.202 52.381 15.91 12.60 0.00 3.67
759 927 1.112950 TATTCCATGGACGCCGTACA 58.887 50.000 15.91 3.81 0.00 2.90
760 928 0.468226 ATTCCATGGACGCCGTACAT 59.532 50.000 15.91 9.66 37.63 2.29
761 929 0.250793 TTCCATGGACGCCGTACATT 59.749 50.000 13.31 0.00 34.46 2.71
762 930 0.250793 TCCATGGACGCCGTACATTT 59.749 50.000 13.31 0.00 34.46 2.32
763 931 1.091537 CCATGGACGCCGTACATTTT 58.908 50.000 13.31 0.00 34.46 1.82
764 932 1.470890 CCATGGACGCCGTACATTTTT 59.529 47.619 13.31 0.00 34.46 1.94
840 1116 1.154197 CTGCCCATGCGTCATCTATG 58.846 55.000 0.00 0.00 41.78 2.23
850 1126 7.387673 CCCATGCGTCATCTATGTATTTTTCTA 59.612 37.037 0.00 0.00 0.00 2.10
887 1165 3.173668 AGTTACAAACACACGCTCTCA 57.826 42.857 0.00 0.00 0.00 3.27
902 1180 2.392662 CTCTCAATCAGCTCACCCCTA 58.607 52.381 0.00 0.00 0.00 3.53
952 1230 0.108396 TGCCTAGTTCTTGCAGCACA 59.892 50.000 0.00 0.00 0.00 4.57
974 1254 7.643764 GCACAAGCGTGACACATATATAAAAAT 59.356 33.333 6.65 0.00 46.80 1.82
975 1255 9.158364 CACAAGCGTGACACATATATAAAAATC 57.842 33.333 6.65 0.00 46.80 2.17
1000 1280 4.431131 CCCCACCGCTTCTGGCAT 62.431 66.667 0.00 0.00 41.91 4.40
1024 1304 1.825191 CACACTTGCACCAGCCAGT 60.825 57.895 0.00 0.00 46.61 4.00
1193 1493 3.077556 CTGGTGCGGCTCTACCCT 61.078 66.667 0.00 0.00 36.10 4.34
1194 1494 1.756950 CTGGTGCGGCTCTACCCTA 60.757 63.158 0.00 0.00 36.10 3.53
1293 1614 1.561643 TCATCTCCCGCTCACTCTTT 58.438 50.000 0.00 0.00 0.00 2.52
1446 1767 4.096003 GTGGCCGCCTTCCTAGCA 62.096 66.667 11.61 0.00 0.00 3.49
1782 3231 3.199891 GCGGTCATAACGGGCCAC 61.200 66.667 4.39 0.00 0.00 5.01
1832 3282 4.742201 GCGAGTGCCTGGCTTCGA 62.742 66.667 33.94 10.77 38.09 3.71
1894 3344 3.315191 GCATGGGTATGATAAGCGTGTTT 59.685 43.478 0.00 0.00 36.36 2.83
1991 3441 6.252995 ACAACCAGGAGCATTTTCCTATAAA 58.747 36.000 0.00 0.00 45.86 1.40
2097 3547 8.823810 ACTTCCCCCATCCTAAAATAAGTATA 57.176 34.615 0.00 0.00 0.00 1.47
2098 3548 8.891501 ACTTCCCCCATCCTAAAATAAGTATAG 58.108 37.037 0.00 0.00 0.00 1.31
2102 3552 7.037586 CCCCCATCCTAAAATAAGTATAGCTGA 60.038 40.741 0.00 0.00 0.00 4.26
2103 3553 8.552296 CCCCATCCTAAAATAAGTATAGCTGAT 58.448 37.037 0.00 0.00 0.00 2.90
2104 3554 9.965902 CCCATCCTAAAATAAGTATAGCTGATT 57.034 33.333 0.00 0.00 29.37 2.57
2151 3601 4.788679 ACATTTATTTTAGGACGGAGGGG 58.211 43.478 0.00 0.00 0.00 4.79
2199 3653 6.848451 TCCTAAAACAAGATATTTCAACGGC 58.152 36.000 0.00 0.00 0.00 5.68
2203 3657 3.016736 ACAAGATATTTCAACGGCCAGG 58.983 45.455 2.24 0.00 0.00 4.45
2204 3658 1.680338 AGATATTTCAACGGCCAGGC 58.320 50.000 1.26 1.26 0.00 4.85
2217 3671 2.452813 CCAGGCGCGATACACACAC 61.453 63.158 12.10 0.00 0.00 3.82
2218 3672 2.125673 AGGCGCGATACACACACC 60.126 61.111 12.10 0.00 0.00 4.16
2257 3718 1.488812 TGCGCCATGGGTCTATAGTTT 59.511 47.619 15.13 0.00 0.00 2.66
2282 4018 1.109323 GCAAATGATTAGGCCCGGCT 61.109 55.000 9.86 0.34 0.00 5.52
2367 4113 2.029518 CAGGCGTCACACTGAGCA 59.970 61.111 0.00 0.00 36.86 4.26
2368 4114 1.375140 CAGGCGTCACACTGAGCAT 60.375 57.895 0.00 0.00 36.86 3.79
2369 4115 1.375140 AGGCGTCACACTGAGCATG 60.375 57.895 0.00 0.00 0.00 4.06
2373 4184 1.713597 CGTCACACTGAGCATGCTAA 58.286 50.000 22.74 13.44 0.00 3.09
2423 4235 1.812571 ACATTGCGACTTTGGCCTTAG 59.187 47.619 3.32 3.42 0.00 2.18
2443 4255 1.332686 GACTCGCCCAACTTCGTTTTT 59.667 47.619 0.00 0.00 0.00 1.94
2445 4257 2.546789 ACTCGCCCAACTTCGTTTTTAG 59.453 45.455 0.00 0.00 0.00 1.85
2446 4258 1.874872 TCGCCCAACTTCGTTTTTAGG 59.125 47.619 0.00 0.00 0.00 2.69
2447 4259 1.605232 CGCCCAACTTCGTTTTTAGGT 59.395 47.619 0.00 0.00 0.00 3.08
2448 4260 2.807392 CGCCCAACTTCGTTTTTAGGTA 59.193 45.455 0.00 0.00 0.00 3.08
2449 4261 3.120442 CGCCCAACTTCGTTTTTAGGTAG 60.120 47.826 0.00 0.00 0.00 3.18
2450 4262 3.365666 GCCCAACTTCGTTTTTAGGTAGC 60.366 47.826 0.00 0.00 0.00 3.58
2451 4263 3.120442 CCCAACTTCGTTTTTAGGTAGCG 60.120 47.826 0.00 0.00 0.00 4.26
2452 4264 3.476181 CAACTTCGTTTTTAGGTAGCGC 58.524 45.455 0.00 0.00 0.00 5.92
2453 4265 2.071540 ACTTCGTTTTTAGGTAGCGCC 58.928 47.619 2.29 0.00 37.58 6.53
2454 4266 1.060122 CTTCGTTTTTAGGTAGCGCCG 59.940 52.381 2.29 0.00 43.70 6.46
2455 4267 0.737019 TCGTTTTTAGGTAGCGCCGG 60.737 55.000 2.29 0.00 43.70 6.13
2456 4268 1.015607 CGTTTTTAGGTAGCGCCGGT 61.016 55.000 2.29 0.00 43.70 5.28
2457 4269 0.723414 GTTTTTAGGTAGCGCCGGTC 59.277 55.000 2.29 0.00 43.70 4.79
2496 4596 4.499188 GCGAGCTTGTTAACCCTTCTTTTT 60.499 41.667 2.48 0.00 0.00 1.94
2499 4628 5.902681 AGCTTGTTAACCCTTCTTTTTGAC 58.097 37.500 2.48 0.00 0.00 3.18
2595 4751 2.932663 CTGAAACACGGCATGGACT 58.067 52.632 0.00 0.00 0.00 3.85
2676 4833 2.250646 GGTTACCTTCAACCGTGGC 58.749 57.895 0.00 0.00 38.74 5.01
2733 4955 2.161855 TGTGTGCAATGGGATGTTCTC 58.838 47.619 0.00 0.00 0.00 2.87
2736 4958 2.225091 TGTGCAATGGGATGTTCTCCTT 60.225 45.455 0.00 0.00 44.28 3.36
2768 4990 2.187163 GGCGAGCTTACCACCTCC 59.813 66.667 1.24 0.00 0.00 4.30
2771 4994 0.107654 GCGAGCTTACCACCTCCATT 60.108 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 41 8.293867 GCAACCTACTTGATGTTTTATGTGTTA 58.706 33.333 0.00 0.00 30.42 2.41
39 42 7.145323 GCAACCTACTTGATGTTTTATGTGTT 58.855 34.615 0.00 0.00 30.42 3.32
40 43 6.264292 TGCAACCTACTTGATGTTTTATGTGT 59.736 34.615 0.00 0.00 30.42 3.72
41 44 6.676950 TGCAACCTACTTGATGTTTTATGTG 58.323 36.000 0.00 0.00 30.42 3.21
42 45 6.892658 TGCAACCTACTTGATGTTTTATGT 57.107 33.333 0.00 0.00 30.42 2.29
43 46 8.586570 TTTTGCAACCTACTTGATGTTTTATG 57.413 30.769 0.00 0.00 30.42 1.90
53 63 4.524328 AGAGGGAATTTTGCAACCTACTTG 59.476 41.667 0.00 0.00 0.00 3.16
57 67 5.249780 TGTAGAGGGAATTTTGCAACCTA 57.750 39.130 0.00 0.00 0.00 3.08
63 73 7.063426 GCAATAGTTTTGTAGAGGGAATTTTGC 59.937 37.037 0.00 0.00 0.00 3.68
100 113 0.443869 CACGGCTTGATCTTCGTTGG 59.556 55.000 0.00 0.00 33.31 3.77
105 118 1.087501 GGTTCCACGGCTTGATCTTC 58.912 55.000 0.00 0.00 0.00 2.87
237 251 3.392947 TGTGTAAGTCCCACATCCTTTCA 59.607 43.478 0.00 0.00 37.88 2.69
249 263 4.466726 AGGGTCACTAAGATGTGTAAGTCC 59.533 45.833 0.00 0.00 38.90 3.85
263 277 3.170991 ACAGACTTAGCAGGGTCACTA 57.829 47.619 5.92 0.00 35.18 2.74
273 287 7.116948 CCATGTGCTAATATGTACAGACTTAGC 59.883 40.741 25.29 25.29 42.80 3.09
303 434 2.825861 TCCTCGTTGGGAAGTTACAC 57.174 50.000 0.00 0.00 36.20 2.90
317 448 4.253685 TCATTTCTTGTTAGGCTTCCTCG 58.746 43.478 0.00 0.00 34.61 4.63
359 490 8.284693 GTCTAGGTTGTTATCGCTAAACAAAAA 58.715 33.333 10.14 1.66 45.56 1.94
364 495 8.693542 TTTAGTCTAGGTTGTTATCGCTAAAC 57.306 34.615 0.00 0.00 0.00 2.01
406 538 3.870633 CTAGTCGAGCTAGTTGGGTTT 57.129 47.619 11.60 0.00 41.68 3.27
427 559 2.302157 ACCTAGTCTTTTTCGGGGTGAG 59.698 50.000 0.00 0.00 0.00 3.51
434 566 5.116680 CACGTAGTTGACCTAGTCTTTTTCG 59.883 44.000 0.00 0.00 41.61 3.46
435 567 6.211515 TCACGTAGTTGACCTAGTCTTTTTC 58.788 40.000 0.00 0.00 41.61 2.29
443 575 7.310664 TCAATAGTTTCACGTAGTTGACCTAG 58.689 38.462 0.00 0.00 41.61 3.02
447 579 8.100306 CGTAATCAATAGTTTCACGTAGTTGAC 58.900 37.037 0.00 0.00 41.61 3.18
449 581 8.165212 TCGTAATCAATAGTTTCACGTAGTTG 57.835 34.615 0.00 0.00 41.61 3.16
450 582 8.922058 ATCGTAATCAATAGTTTCACGTAGTT 57.078 30.769 0.00 0.00 41.61 2.24
455 587 7.422462 CACACAATCGTAATCAATAGTTTCACG 59.578 37.037 0.00 0.00 0.00 4.35
558 723 9.686683 ATTGTCTATGTGCCTAGTAAAGAAAAT 57.313 29.630 0.00 0.00 0.00 1.82
563 728 9.469807 CTCTAATTGTCTATGTGCCTAGTAAAG 57.530 37.037 0.00 0.00 0.00 1.85
566 731 8.762481 TTCTCTAATTGTCTATGTGCCTAGTA 57.238 34.615 0.00 0.00 0.00 1.82
567 732 7.661536 TTCTCTAATTGTCTATGTGCCTAGT 57.338 36.000 0.00 0.00 0.00 2.57
568 733 9.553064 AATTTCTCTAATTGTCTATGTGCCTAG 57.447 33.333 0.00 0.00 35.15 3.02
569 734 9.547753 GAATTTCTCTAATTGTCTATGTGCCTA 57.452 33.333 0.00 0.00 36.59 3.93
570 735 7.225538 CGAATTTCTCTAATTGTCTATGTGCCT 59.774 37.037 0.00 0.00 36.59 4.75
595 760 9.265938 CATAATTGTGTGTCTGAATTTTAGTCG 57.734 33.333 0.00 0.00 0.00 4.18
670 837 9.866655 AAGTGATTATCTCCCATTTAATTAGCA 57.133 29.630 0.00 0.00 0.00 3.49
721 889 7.934457 TGGAATACAGTTACCTCGTTACTATC 58.066 38.462 0.00 0.00 0.00 2.08
722 890 7.886629 TGGAATACAGTTACCTCGTTACTAT 57.113 36.000 0.00 0.00 0.00 2.12
723 891 7.201848 CCATGGAATACAGTTACCTCGTTACTA 60.202 40.741 5.56 0.00 0.00 1.82
724 892 6.406624 CCATGGAATACAGTTACCTCGTTACT 60.407 42.308 5.56 0.00 0.00 2.24
725 893 5.751990 CCATGGAATACAGTTACCTCGTTAC 59.248 44.000 5.56 0.00 0.00 2.50
726 894 5.657745 TCCATGGAATACAGTTACCTCGTTA 59.342 40.000 13.46 0.00 0.00 3.18
727 895 4.468510 TCCATGGAATACAGTTACCTCGTT 59.531 41.667 13.46 0.00 0.00 3.85
728 896 4.028131 TCCATGGAATACAGTTACCTCGT 58.972 43.478 13.46 0.00 0.00 4.18
729 897 4.369182 GTCCATGGAATACAGTTACCTCG 58.631 47.826 18.20 0.00 0.00 4.63
730 898 4.369182 CGTCCATGGAATACAGTTACCTC 58.631 47.826 18.20 0.00 0.00 3.85
731 899 3.431766 GCGTCCATGGAATACAGTTACCT 60.432 47.826 18.20 0.00 0.00 3.08
732 900 2.870411 GCGTCCATGGAATACAGTTACC 59.130 50.000 18.20 0.00 0.00 2.85
733 901 2.870411 GGCGTCCATGGAATACAGTTAC 59.130 50.000 18.20 0.00 0.00 2.50
734 902 2.482316 CGGCGTCCATGGAATACAGTTA 60.482 50.000 18.20 0.00 0.00 2.24
735 903 1.742411 CGGCGTCCATGGAATACAGTT 60.742 52.381 18.20 0.00 0.00 3.16
736 904 0.179084 CGGCGTCCATGGAATACAGT 60.179 55.000 18.20 0.00 0.00 3.55
737 905 0.179084 ACGGCGTCCATGGAATACAG 60.179 55.000 18.20 11.88 0.00 2.74
738 906 1.112950 TACGGCGTCCATGGAATACA 58.887 50.000 19.21 0.00 0.00 2.29
739 907 1.202440 TGTACGGCGTCCATGGAATAC 60.202 52.381 19.21 13.87 0.00 1.89
740 908 1.112950 TGTACGGCGTCCATGGAATA 58.887 50.000 19.21 1.42 0.00 1.75
741 909 0.468226 ATGTACGGCGTCCATGGAAT 59.532 50.000 19.21 0.00 0.00 3.01
742 910 0.250793 AATGTACGGCGTCCATGGAA 59.749 50.000 18.89 0.00 0.00 3.53
743 911 0.250793 AAATGTACGGCGTCCATGGA 59.749 50.000 18.89 11.44 0.00 3.41
744 912 1.091537 AAAATGTACGGCGTCCATGG 58.908 50.000 18.89 4.97 0.00 3.66
745 913 2.418628 AGAAAAATGTACGGCGTCCATG 59.581 45.455 18.89 0.00 0.00 3.66
746 914 2.706890 AGAAAAATGTACGGCGTCCAT 58.293 42.857 19.21 15.47 0.00 3.41
747 915 2.172851 AGAAAAATGTACGGCGTCCA 57.827 45.000 19.21 13.23 0.00 4.02
748 916 2.413634 CCAAGAAAAATGTACGGCGTCC 60.414 50.000 19.21 5.43 0.00 4.79
749 917 2.846693 CCAAGAAAAATGTACGGCGTC 58.153 47.619 19.21 9.31 0.00 5.19
750 918 1.068816 GCCAAGAAAAATGTACGGCGT 60.069 47.619 19.64 19.64 0.00 5.68
751 919 1.199097 AGCCAAGAAAAATGTACGGCG 59.801 47.619 4.80 4.80 42.90 6.46
752 920 4.632538 ATAGCCAAGAAAAATGTACGGC 57.367 40.909 0.00 0.00 38.36 5.68
753 921 7.730364 ATCTATAGCCAAGAAAAATGTACGG 57.270 36.000 0.00 0.00 0.00 4.02
754 922 9.477484 ACTATCTATAGCCAAGAAAAATGTACG 57.523 33.333 0.00 0.00 33.68 3.67
760 928 9.745880 CTCGTTACTATCTATAGCCAAGAAAAA 57.254 33.333 0.00 0.00 33.68 1.94
761 929 8.358148 CCTCGTTACTATCTATAGCCAAGAAAA 58.642 37.037 0.00 0.00 33.68 2.29
762 930 7.504911 ACCTCGTTACTATCTATAGCCAAGAAA 59.495 37.037 0.00 0.00 33.68 2.52
763 931 7.002879 ACCTCGTTACTATCTATAGCCAAGAA 58.997 38.462 0.00 0.00 33.68 2.52
764 932 6.540995 ACCTCGTTACTATCTATAGCCAAGA 58.459 40.000 0.00 0.00 33.68 3.02
850 1126 7.643569 TTGTAACTTTGTATGCATGGATGAT 57.356 32.000 10.16 0.00 0.00 2.45
887 1165 1.348775 GGCCTAGGGGTGAGCTGATT 61.349 60.000 11.72 0.00 34.45 2.57
921 1199 1.839424 ACTAGGCAGCAATCAAACCC 58.161 50.000 0.00 0.00 0.00 4.11
952 1230 9.325198 TCAGATTTTTATATATGTGTCACGCTT 57.675 29.630 0.00 0.00 0.00 4.68
974 1254 3.311110 GCGGTGGGGAGTGTCAGA 61.311 66.667 0.00 0.00 0.00 3.27
975 1255 2.788191 GAAGCGGTGGGGAGTGTCAG 62.788 65.000 0.00 0.00 0.00 3.51
1000 1280 1.662517 CTGGTGCAAGTGTGTGTACA 58.337 50.000 0.00 0.00 35.99 2.90
1024 1304 2.512355 TACACAGCTCGGTTGGCCA 61.512 57.895 0.00 0.00 34.09 5.36
1193 1493 1.651240 GCCGTCGCCACAGTACTCTA 61.651 60.000 0.00 0.00 0.00 2.43
1194 1494 2.991076 GCCGTCGCCACAGTACTCT 61.991 63.158 0.00 0.00 0.00 3.24
1389 1710 2.639286 CTGCTTGTGGTGCCGAAC 59.361 61.111 0.00 0.00 0.00 3.95
1446 1767 0.117140 TGGTCTCATGGGAGGTCTGT 59.883 55.000 0.00 0.00 41.69 3.41
1782 3231 1.094073 CCGCTGCTGAAGGATTCCAG 61.094 60.000 5.29 0.00 46.93 3.86
1827 3277 4.526970 GATGTTGGTGATCACATCGAAG 57.473 45.455 26.47 0.00 31.25 3.79
1832 3282 3.333029 TGACGATGTTGGTGATCACAT 57.667 42.857 26.47 11.92 0.00 3.21
1894 3344 1.205417 GTAAAACCCGATCCGGTCAGA 59.795 52.381 6.18 0.00 46.80 3.27
1955 3405 1.160137 CTGGTTGTAGCAGTCAAGGC 58.840 55.000 0.00 0.00 38.80 4.35
2075 3525 7.029390 AGCTATACTTATTTTAGGATGGGGGA 58.971 38.462 0.00 0.00 0.00 4.81
2078 3528 9.965902 AATCAGCTATACTTATTTTAGGATGGG 57.034 33.333 0.00 0.00 0.00 4.00
2144 3594 6.429521 TCTAAATCTTTTATACCCCCTCCG 57.570 41.667 0.00 0.00 0.00 4.63
2199 3653 2.125713 TGTGTGTATCGCGCCTGG 60.126 61.111 0.00 0.00 0.00 4.45
2203 3657 0.247655 CAATGGTGTGTGTATCGCGC 60.248 55.000 0.00 0.00 36.46 6.86
2204 3658 1.075542 ACAATGGTGTGTGTATCGCG 58.924 50.000 0.00 0.00 36.31 5.87
2217 3671 1.271163 ACACCGAGTAACCCACAATGG 60.271 52.381 0.00 0.00 37.25 3.16
2218 3672 1.804151 CACACCGAGTAACCCACAATG 59.196 52.381 0.00 0.00 0.00 2.82
2257 3718 2.699846 GGGCCTAATCATTTGCATTGGA 59.300 45.455 0.84 0.00 0.00 3.53
2282 4018 1.278985 ACATCATGCACGGAAGAGGAA 59.721 47.619 0.00 0.00 0.00 3.36
2356 4102 2.676176 GCTCTTAGCATGCTCAGTGTGA 60.676 50.000 26.57 12.78 41.89 3.58
2369 4115 1.162181 TGCGATGGCATGCTCTTAGC 61.162 55.000 18.92 16.52 46.21 3.09
2443 4255 0.533755 GAGTAGACCGGCGCTACCTA 60.534 60.000 23.90 1.20 39.17 3.08
2445 4257 2.720605 GAGTAGACCGGCGCTACC 59.279 66.667 23.90 15.26 39.17 3.18
2446 4258 2.327244 CGAGTAGACCGGCGCTAC 59.673 66.667 21.42 21.42 38.76 3.58
2447 4259 3.580193 GCGAGTAGACCGGCGCTA 61.580 66.667 7.64 7.51 45.41 4.26
2450 4262 4.111016 TGTGCGAGTAGACCGGCG 62.111 66.667 0.00 0.00 0.00 6.46
2451 4263 2.202623 CTGTGCGAGTAGACCGGC 60.203 66.667 0.00 0.00 0.00 6.13
2452 4264 2.202623 GCTGTGCGAGTAGACCGG 60.203 66.667 0.00 0.00 0.00 5.28
2453 4265 1.073216 CAAGCTGTGCGAGTAGACCG 61.073 60.000 0.00 0.00 0.00 4.79
2454 4266 0.737715 CCAAGCTGTGCGAGTAGACC 60.738 60.000 0.00 0.00 0.00 3.85
2455 4267 1.355066 GCCAAGCTGTGCGAGTAGAC 61.355 60.000 0.00 0.00 0.00 2.59
2456 4268 1.079819 GCCAAGCTGTGCGAGTAGA 60.080 57.895 0.00 0.00 0.00 2.59
2457 4269 3.479370 GCCAAGCTGTGCGAGTAG 58.521 61.111 0.00 0.00 0.00 2.57
2499 4628 1.227263 CGCAAGAGTACCGATGGGG 60.227 63.158 0.00 0.00 41.03 4.96
2509 4638 1.376424 CCAGTCATGCCGCAAGAGT 60.376 57.895 0.00 0.00 43.02 3.24
2595 4751 6.262601 GCTACAAAACAAACTGCAGAACTTA 58.737 36.000 23.35 0.00 0.00 2.24
2676 4833 0.835276 TCCATCTGCTCACCCTCATG 59.165 55.000 0.00 0.00 0.00 3.07
2733 4955 1.749063 GCCGAATTTGAAGGGGTAAGG 59.251 52.381 0.00 0.00 0.00 2.69
2736 4958 0.614294 TCGCCGAATTTGAAGGGGTA 59.386 50.000 0.00 0.00 38.83 3.69
2808 5031 6.153510 TCTCTAACTGTCTACGTGTCCTAGTA 59.846 42.308 0.00 0.00 0.00 1.82
2815 5038 6.072838 TCGAATTTCTCTAACTGTCTACGTGT 60.073 38.462 0.00 0.00 0.00 4.49
2940 5163 8.518430 TCTATAGCCAAGAAACAATTTATGCA 57.482 30.769 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.