Multiple sequence alignment - TraesCS7B01G079400

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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 TraesCS7B01G079400 chr7B 100.000 2858 0 0 1 2858 89561663 89558806 0.000000e+00 5278.0
1 TraesCS7B01G079400 chr7B 90.405 1063 94 7 987 2042 89656973 89655912 0.000000e+00 1391.0
2 TraesCS7B01G079400 chr7B 81.192 1393 226 31 622 1994 89542944 89541568 0.000000e+00 1088.0
3 TraesCS7B01G079400 chr7B 93.484 353 20 3 621 971 89657521 89657170 3.260000e-144 521.0
4 TraesCS7B01G079400 chr7B 87.003 377 44 4 2095 2468 89655892 89655518 1.220000e-113 420.0
5 TraesCS7B01G079400 chr7B 85.593 118 16 1 2476 2592 89655475 89655358 3.870000e-24 122.0
6 TraesCS7B01G079400 chr7D 88.308 2506 219 37 5 2468 127738219 127735746 0.000000e+00 2937.0
7 TraesCS7B01G079400 chr7D 85.884 2522 240 55 4 2468 127734011 127731549 0.000000e+00 2579.0
8 TraesCS7B01G079400 chr7D 88.389 1490 150 13 987 2468 127753100 127751626 0.000000e+00 1772.0
9 TraesCS7B01G079400 chr7D 87.893 1495 146 21 987 2468 127765601 127764129 0.000000e+00 1725.0
10 TraesCS7B01G079400 chr7D 89.575 1199 107 12 1275 2468 127730475 127729290 0.000000e+00 1506.0
11 TraesCS7B01G079400 chr7D 85.996 1421 127 35 93 1496 127700860 127699495 0.000000e+00 1456.0
12 TraesCS7B01G079400 chr7D 88.242 944 94 10 1532 2468 127699496 127698563 0.000000e+00 1112.0
13 TraesCS7B01G079400 chr7D 86.725 806 69 21 176 971 127754053 127753276 0.000000e+00 861.0
14 TraesCS7B01G079400 chr7D 81.352 917 159 11 1082 1994 127650431 127649523 0.000000e+00 736.0
15 TraesCS7B01G079400 chr7D 94.034 352 20 1 621 971 127766141 127765790 1.510000e-147 532.0
16 TraesCS7B01G079400 chr7D 88.073 218 23 1 2640 2854 127764931 127764714 3.650000e-64 255.0
17 TraesCS7B01G079400 chr7D 100.000 29 0 0 7 35 127700902 127700874 1.000000e-03 54.7
18 TraesCS7B01G079400 chr7A 90.101 1192 97 9 987 2169 128510910 128509731 0.000000e+00 1528.0
19 TraesCS7B01G079400 chr7A 83.680 913 142 6 1085 1994 128405564 128404656 0.000000e+00 854.0
20 TraesCS7B01G079400 chr7A 94.318 352 19 1 621 971 128511406 128511055 3.240000e-149 538.0
21 TraesCS7B01G079400 chr7A 88.636 352 38 2 622 971 128406114 128405763 7.320000e-116 427.0
22 TraesCS7B01G079400 chr3A 92.675 314 21 2 2157 2468 672876465 672876778 4.340000e-123 451.0
23 TraesCS7B01G079400 chr2D 92.675 314 21 2 2157 2468 630272256 630271943 4.340000e-123 451.0
24 TraesCS7B01G079400 chrUn 92.357 314 22 2 2157 2468 371050417 371050104 2.020000e-121 446.0


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 TraesCS7B01G079400 chr7B 89558806 89561663 2857 True 5278.000000 5278 100.000000 1 2858 1 chr7B.!!$R2 2857
1 TraesCS7B01G079400 chr7B 89541568 89542944 1376 True 1088.000000 1088 81.192000 622 1994 1 chr7B.!!$R1 1372
2 TraesCS7B01G079400 chr7B 89655358 89657521 2163 True 613.500000 1391 89.121250 621 2592 4 chr7B.!!$R3 1971
3 TraesCS7B01G079400 chr7D 127729290 127738219 8929 True 2340.666667 2937 87.922333 4 2468 3 chr7D.!!$R3 2464
4 TraesCS7B01G079400 chr7D 127751626 127754053 2427 True 1316.500000 1772 87.557000 176 2468 2 chr7D.!!$R4 2292
5 TraesCS7B01G079400 chr7D 127698563 127700902 2339 True 874.233333 1456 91.412667 7 2468 3 chr7D.!!$R2 2461
6 TraesCS7B01G079400 chr7D 127764129 127766141 2012 True 837.333333 1725 90.000000 621 2854 3 chr7D.!!$R5 2233
7 TraesCS7B01G079400 chr7D 127649523 127650431 908 True 736.000000 736 81.352000 1082 1994 1 chr7D.!!$R1 912
8 TraesCS7B01G079400 chr7A 128509731 128511406 1675 True 1033.000000 1528 92.209500 621 2169 2 chr7A.!!$R2 1548
9 TraesCS7B01G079400 chr7A 128404656 128406114 1458 True 640.500000 854 86.158000 622 1994 2 chr7A.!!$R1 1372

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
439 455 0.310854 CACAGTGGGAAAAGAACGCC 59.689 55.0 0.0 0.0 0.00 5.68 F
1215 5740 0.308068 ACGAGATACCGCTGATCGTG 59.692 55.0 0.0 0.0 44.23 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 6171 0.325933 TCCTTCCTCTCGGTCGTACA 59.674 55.0 0.0 0.0 0.00 2.90 R
2609 7188 0.035439 AACACCTACCTGGAATGGCG 60.035 55.0 0.0 0.0 39.71 5.69 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
159 163 3.058293 GTCGTGATGCTTGTGAAATTCCA 60.058 43.478 0.00 0.00 0.00 3.53
165 169 7.073265 GTGATGCTTGTGAAATTCCATTTTTG 58.927 34.615 0.00 0.00 31.47 2.44
168 173 5.759273 TGCTTGTGAAATTCCATTTTTGGAG 59.241 36.000 0.00 0.00 39.43 3.86
238 245 5.124457 TCATCGCTTCTATGATGATCGATCA 59.876 40.000 29.09 29.09 44.41 2.92
252 259 2.076100 TCGATCACAATCAGCACCAAC 58.924 47.619 0.00 0.00 31.76 3.77
256 263 0.599558 CACAATCAGCACCAACCTGG 59.400 55.000 0.00 0.00 45.02 4.45
301 315 1.457346 CTGGTGCCTTGATGAGAACC 58.543 55.000 0.00 0.00 34.33 3.62
335 349 3.008049 ACTGTATCTTGTTCCCACAGGAC 59.992 47.826 5.17 0.00 43.90 3.85
351 365 0.741915 GGACTCGCTTCTCTTCGGAT 59.258 55.000 0.00 0.00 0.00 4.18
423 439 2.611751 CTGGTCAAACAATGTCGACACA 59.388 45.455 22.71 9.89 36.78 3.72
434 450 1.483004 TGTCGACACAGTGGGAAAAGA 59.517 47.619 15.76 0.00 0.00 2.52
439 455 0.310854 CACAGTGGGAAAAGAACGCC 59.689 55.000 0.00 0.00 0.00 5.68
481 503 7.174946 CCGGCACCTATAAATACAATCTTCATT 59.825 37.037 0.00 0.00 0.00 2.57
483 505 8.230486 GGCACCTATAAATACAATCTTCATTCG 58.770 37.037 0.00 0.00 0.00 3.34
507 529 2.632512 TGTTCAGCCACAGACATACAGA 59.367 45.455 0.00 0.00 0.00 3.41
508 530 2.996621 GTTCAGCCACAGACATACAGAC 59.003 50.000 0.00 0.00 0.00 3.51
543 565 3.544684 TCAGAAGCAAGAAACAGAGCAA 58.455 40.909 0.00 0.00 0.00 3.91
552 574 5.450550 GCAAGAAACAGAGCAAGGTTTTAGT 60.451 40.000 0.00 0.00 37.35 2.24
563 585 4.686091 GCAAGGTTTTAGTGATTCCTTTGC 59.314 41.667 0.00 0.00 36.52 3.68
564 586 5.738783 GCAAGGTTTTAGTGATTCCTTTGCA 60.739 40.000 0.00 0.00 36.52 4.08
565 587 6.279882 CAAGGTTTTAGTGATTCCTTTGCAA 58.720 36.000 0.00 0.00 36.52 4.08
576 603 5.883115 TGATTCCTTTGCAATACCATCGTAA 59.117 36.000 0.00 0.00 0.00 3.18
583 611 7.011950 CCTTTGCAATACCATCGTAATACTTGA 59.988 37.037 0.00 0.00 0.00 3.02
803 836 4.247380 GGGCGGCCTCCTCATCAG 62.247 72.222 22.87 0.00 0.00 2.90
972 1005 1.190178 GGGTCTCCACCAACGGTACT 61.190 60.000 0.00 0.00 45.94 2.73
975 1008 1.067776 GTCTCCACCAACGGTACTCTG 60.068 57.143 0.00 0.00 32.11 3.35
1018 1326 6.327177 CATTCATGCTATTTTGTGTTGCTC 57.673 37.500 0.00 0.00 0.00 4.26
1027 1335 8.397906 TGCTATTTTGTGTTGCTCAACTATATC 58.602 33.333 13.16 1.65 41.67 1.63
1147 1466 2.105134 ACCGACAAACAGATAACACCCA 59.895 45.455 0.00 0.00 0.00 4.51
1151 5676 4.215399 CGACAAACAGATAACACCCAATGT 59.785 41.667 0.00 0.00 46.42 2.71
1185 5710 0.543410 TCTACTCCAAGCCCCGACAA 60.543 55.000 0.00 0.00 0.00 3.18
1189 5714 1.228124 TCCAAGCCCCGACAACTTG 60.228 57.895 0.00 0.00 40.36 3.16
1215 5740 0.308068 ACGAGATACCGCTGATCGTG 59.692 55.000 0.00 0.00 44.23 4.35
1330 5855 4.218635 TCATGAAAGACAGCTCTAACGACT 59.781 41.667 0.00 0.00 0.00 4.18
1450 5975 4.743057 ATCAGATTGTCTCCATTCGTGA 57.257 40.909 0.00 0.00 0.00 4.35
1530 6055 2.887152 ACTCAACAAGCATCAAGGGTTC 59.113 45.455 0.00 0.00 0.00 3.62
1646 6171 2.033448 TTTCATTGCCGCCGGAGT 59.967 55.556 7.68 0.00 0.00 3.85
1650 6175 2.125269 ATTGCCGCCGGAGTGTAC 60.125 61.111 7.68 0.00 0.00 2.90
1824 6349 2.028112 TCCTGTCATTGGCTACACAGAC 60.028 50.000 10.25 0.00 38.90 3.51
1885 6413 5.178797 CCCACTCGACTTGAATTAGTGATT 58.821 41.667 0.00 0.00 39.93 2.57
1890 6418 6.091441 ACTCGACTTGAATTAGTGATTTGCTC 59.909 38.462 0.00 0.00 0.00 4.26
1930 6461 9.687210 ATGTGATGATTTATTCAATGTGTATGC 57.313 29.630 0.00 0.00 38.03 3.14
1931 6462 8.684520 TGTGATGATTTATTCAATGTGTATGCA 58.315 29.630 0.00 0.00 38.03 3.96
1990 6525 8.472007 TTTACTTTTGTTCTCCCATGTAATGT 57.528 30.769 0.00 0.00 44.81 2.71
1996 6531 7.624360 TTGTTCTCCCATGTAATGTCAATAC 57.376 36.000 0.00 0.00 44.81 1.89
2002 6537 6.174049 TCCCATGTAATGTCAATACGTCAAA 58.826 36.000 0.00 0.00 44.81 2.69
2006 6541 9.995957 CCATGTAATGTCAATACGTCAAAATAA 57.004 29.630 0.00 0.00 44.81 1.40
2053 6588 7.719633 ACAACATTGTCTTCAGTTACCTGTAAT 59.280 33.333 0.00 0.00 36.50 1.89
2055 6590 9.959721 AACATTGTCTTCAGTTACCTGTAATAT 57.040 29.630 0.00 0.00 39.82 1.28
2082 6617 4.277476 TCTATTGCCATGGTACCCAAAAG 58.723 43.478 14.67 0.23 36.95 2.27
2083 6618 1.638529 TTGCCATGGTACCCAAAAGG 58.361 50.000 14.67 5.18 36.95 3.11
2084 6619 0.902516 TGCCATGGTACCCAAAAGGC 60.903 55.000 14.67 15.15 44.55 4.35
2085 6620 1.613317 GCCATGGTACCCAAAAGGCC 61.613 60.000 14.67 0.00 41.16 5.19
2086 6621 0.252012 CCATGGTACCCAAAAGGCCA 60.252 55.000 10.07 0.00 40.58 5.36
2087 6622 1.638529 CATGGTACCCAAAAGGCCAA 58.361 50.000 10.07 0.00 40.58 4.52
2088 6623 1.974236 CATGGTACCCAAAAGGCCAAA 59.026 47.619 10.07 0.00 40.58 3.28
2089 6624 2.176247 TGGTACCCAAAAGGCCAAAA 57.824 45.000 10.07 0.00 40.58 2.44
2101 6636 4.607024 CCAAAAAGTGGTGCGTCG 57.393 55.556 0.00 0.00 43.20 5.12
2104 6639 1.187715 CAAAAAGTGGTGCGTCGTTG 58.812 50.000 0.00 0.00 0.00 4.10
2121 6656 1.864082 GTTGCCGGTTGGTTTCATTTG 59.136 47.619 1.90 0.00 37.67 2.32
2127 6662 3.574614 CGGTTGGTTTCATTTGGATGAC 58.425 45.455 0.00 0.00 41.84 3.06
2160 6696 3.904717 CCTATCCGGGCTATCTGATAGT 58.095 50.000 22.12 7.33 35.29 2.12
2163 6699 1.147191 TCCGGGCTATCTGATAGTGGT 59.853 52.381 22.12 0.00 35.29 4.16
2191 6727 3.193267 CAGCTGCAAGGGCTATAACAAAA 59.807 43.478 0.00 0.00 41.91 2.44
2197 6733 6.162777 TGCAAGGGCTATAACAAAATTTGTC 58.837 36.000 12.11 0.00 41.55 3.18
2198 6735 5.580691 GCAAGGGCTATAACAAAATTTGTCC 59.419 40.000 12.11 8.24 39.09 4.02
2202 6740 7.158697 AGGGCTATAACAAAATTTGTCCAAAC 58.841 34.615 12.11 2.69 44.59 2.93
2218 6756 7.831691 TGTCCAAACATCTCCTTTTAATTGA 57.168 32.000 0.00 0.00 0.00 2.57
2220 6758 6.801862 GTCCAAACATCTCCTTTTAATTGACG 59.198 38.462 0.00 0.00 0.00 4.35
2370 6911 9.561069 AAATAGACACTCAAAAGAAGTACATGT 57.439 29.630 2.69 2.69 0.00 3.21
2518 7096 8.746922 TGTGATTCTTTAGTTATTTACGTCGT 57.253 30.769 2.21 2.21 0.00 4.34
2521 7099 9.409312 TGATTCTTTAGTTATTTACGTCGTTGA 57.591 29.630 1.78 0.00 0.00 3.18
2526 7104 7.975866 TTAGTTATTTACGTCGTTGATCCTC 57.024 36.000 1.78 0.00 0.00 3.71
2527 7105 6.205101 AGTTATTTACGTCGTTGATCCTCT 57.795 37.500 1.78 0.00 0.00 3.69
2529 7107 4.985538 ATTTACGTCGTTGATCCTCTCT 57.014 40.909 1.78 0.00 0.00 3.10
2530 7108 3.759527 TTACGTCGTTGATCCTCTCTG 57.240 47.619 1.78 0.00 0.00 3.35
2533 7111 0.532573 GTCGTTGATCCTCTCTGGCA 59.467 55.000 0.00 0.00 35.26 4.92
2561 7140 1.766059 TGGGACACCACACAGCTCT 60.766 57.895 0.00 0.00 43.37 4.09
2574 7153 0.873743 CAGCTCTTAGGCGCTGCTAC 60.874 60.000 7.64 0.00 45.90 3.58
2592 7171 2.898729 ACATCTAGTTGGCCTCGATG 57.101 50.000 3.32 10.96 44.78 3.84
2593 7172 2.388735 ACATCTAGTTGGCCTCGATGA 58.611 47.619 19.59 8.43 42.95 2.92
2594 7173 2.968574 ACATCTAGTTGGCCTCGATGAT 59.031 45.455 19.59 9.97 42.95 2.45
2595 7174 3.244009 ACATCTAGTTGGCCTCGATGATG 60.244 47.826 19.59 19.50 42.95 3.07
2597 7176 3.562182 TCTAGTTGGCCTCGATGATGTA 58.438 45.455 3.32 0.00 0.00 2.29
2600 7179 3.470709 AGTTGGCCTCGATGATGTATTG 58.529 45.455 3.32 0.00 0.00 1.90
2601 7180 3.118261 AGTTGGCCTCGATGATGTATTGT 60.118 43.478 3.32 0.00 0.00 2.71
2602 7181 2.837498 TGGCCTCGATGATGTATTGTG 58.163 47.619 3.32 0.00 0.00 3.33
2603 7182 1.532868 GGCCTCGATGATGTATTGTGC 59.467 52.381 0.00 0.00 0.00 4.57
2606 7185 3.721035 CCTCGATGATGTATTGTGCTGA 58.279 45.455 0.00 0.00 0.00 4.26
2609 7188 2.347939 CGATGATGTATTGTGCTGACGC 60.348 50.000 0.00 0.00 0.00 5.19
2625 7204 2.590092 GCGCCATTCCAGGTAGGT 59.410 61.111 0.00 0.00 39.02 3.08
2627 7206 1.602237 CGCCATTCCAGGTAGGTGT 59.398 57.895 0.00 0.00 39.02 4.16
2629 7208 1.463674 GCCATTCCAGGTAGGTGTTG 58.536 55.000 0.00 0.00 39.02 3.33
2638 8479 0.389948 GGTAGGTGTTGTGCTCGAGG 60.390 60.000 15.58 0.00 0.00 4.63
2658 8499 1.111277 GGAAGGCAACAAAGTGGTGT 58.889 50.000 0.00 0.00 37.40 4.16
2663 8504 0.951558 GCAACAAAGTGGTGTCCGAT 59.048 50.000 0.00 0.00 37.40 4.18
2671 8512 1.146041 TGGTGTCCGATGGCTATGC 59.854 57.895 0.00 0.00 0.00 3.14
2678 8519 1.547820 TCCGATGGCTATGCTGATCTC 59.452 52.381 0.00 0.00 0.00 2.75
2684 8525 0.864455 GCTATGCTGATCTCGTTGCC 59.136 55.000 0.00 0.00 0.00 4.52
2687 8528 3.616076 GCTATGCTGATCTCGTTGCCTAT 60.616 47.826 0.00 0.00 0.00 2.57
2705 8546 0.849417 ATGGGAGGATCTTTCTGGCC 59.151 55.000 0.00 0.00 33.73 5.36
2720 8561 2.905415 TGGCCAATCCAGATTTGACT 57.095 45.000 0.61 0.00 40.72 3.41
2739 8580 4.022464 ACTAAGAGATTTGAGCTCGACG 57.978 45.455 9.64 0.00 37.46 5.12
2756 8597 2.993899 CGACGCTCCTTTGAACAAGTAT 59.006 45.455 0.00 0.00 0.00 2.12
2768 8609 1.519408 ACAAGTATGACCGCAACACC 58.481 50.000 0.00 0.00 0.00 4.16
2780 8621 0.512952 GCAACACCTTCTACACGCAG 59.487 55.000 0.00 0.00 0.00 5.18
2783 8624 0.317479 ACACCTTCTACACGCAGGAC 59.683 55.000 0.00 0.00 29.82 3.85
2784 8625 0.389948 CACCTTCTACACGCAGGACC 60.390 60.000 0.00 0.00 29.82 4.46
2787 8628 1.471119 CTTCTACACGCAGGACCCTA 58.529 55.000 0.00 0.00 0.00 3.53
2792 8633 0.753262 ACACGCAGGACCCTATCATC 59.247 55.000 0.00 0.00 0.00 2.92
2819 8660 6.995091 GCTACACAGATTATCCTTTCCTTGAT 59.005 38.462 0.00 0.00 0.00 2.57
2825 8666 4.860802 TTATCCTTTCCTTGATGGCTCA 57.139 40.909 0.00 0.00 35.26 4.26
2831 8672 2.519771 TCCTTGATGGCTCAAATGCT 57.480 45.000 2.01 0.00 40.78 3.79
2845 8686 4.183865 TCAAATGCTGAGTAGTTCATCCG 58.816 43.478 0.00 0.00 34.68 4.18
2849 8690 1.135139 GCTGAGTAGTTCATCCGCTCA 59.865 52.381 0.00 0.00 34.68 4.26
2854 8695 4.246458 GAGTAGTTCATCCGCTCAACTTT 58.754 43.478 0.00 0.00 32.56 2.66
2855 8696 4.246458 AGTAGTTCATCCGCTCAACTTTC 58.754 43.478 0.00 0.00 32.56 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.019769 TGTTGTTTAAAGTTAAAACCAGTTGC 57.980 30.769 0.00 0.00 34.71 4.17
123 124 7.929941 AGCATCACGACAAGATCTCTATATA 57.070 36.000 0.00 0.00 0.00 0.86
126 127 5.163468 ACAAGCATCACGACAAGATCTCTAT 60.163 40.000 0.00 0.00 0.00 1.98
159 163 2.858745 ACAGCGTGTACCTCCAAAAAT 58.141 42.857 0.00 0.00 0.00 1.82
184 189 0.984230 TGTGTCCTAGCCTTTCTGGG 59.016 55.000 0.00 0.00 44.20 4.45
224 231 5.636543 GTGCTGATTGTGATCGATCATCATA 59.363 40.000 29.53 17.26 43.72 2.15
228 235 3.136763 GGTGCTGATTGTGATCGATCAT 58.863 45.455 29.53 15.25 41.80 2.45
238 245 3.040965 CCAGGTTGGTGCTGATTGT 57.959 52.632 0.00 0.00 31.35 2.71
286 300 1.299648 CCGGGTTCTCATCAAGGCA 59.700 57.895 0.00 0.00 0.00 4.75
335 349 1.863624 GCTCATCCGAAGAGAAGCGAG 60.864 57.143 4.80 0.00 35.09 5.03
423 439 1.599797 CGGGCGTTCTTTTCCCACT 60.600 57.895 0.00 0.00 40.05 4.00
481 503 0.950555 GTCTGTGGCTGAACATGCGA 60.951 55.000 0.00 0.00 0.00 5.10
483 505 1.171308 ATGTCTGTGGCTGAACATGC 58.829 50.000 0.00 0.00 0.00 4.06
507 529 4.464244 TGCTTCTGAACTATGCTCTGTAGT 59.536 41.667 1.83 0.00 33.98 2.73
508 530 5.003692 TGCTTCTGAACTATGCTCTGTAG 57.996 43.478 1.83 0.00 0.00 2.74
543 565 6.670695 ATTGCAAAGGAATCACTAAAACCT 57.329 33.333 1.71 0.00 0.00 3.50
552 574 4.269183 ACGATGGTATTGCAAAGGAATCA 58.731 39.130 1.71 0.00 0.00 2.57
563 585 6.346919 GCAGCTCAAGTATTACGATGGTATTG 60.347 42.308 0.00 0.00 0.00 1.90
564 586 5.696724 GCAGCTCAAGTATTACGATGGTATT 59.303 40.000 0.00 0.00 0.00 1.89
565 587 5.221441 TGCAGCTCAAGTATTACGATGGTAT 60.221 40.000 0.00 0.00 0.00 2.73
1018 1326 4.222810 TCGGTCATGGGGATGATATAGTTG 59.777 45.833 0.00 0.00 32.61 3.16
1027 1335 4.144297 ACAATTAATCGGTCATGGGGATG 58.856 43.478 0.00 0.00 0.00 3.51
1147 1466 0.038166 ACCATGCCGGACTCAACATT 59.962 50.000 5.05 0.00 38.63 2.71
1151 5676 0.535335 GTAGACCATGCCGGACTCAA 59.465 55.000 5.05 0.00 40.51 3.02
1185 5710 3.834610 CGGTATCTCGTCTGTTTCAAGT 58.165 45.455 0.00 0.00 0.00 3.16
1189 5714 2.159421 TCAGCGGTATCTCGTCTGTTTC 60.159 50.000 0.00 0.00 36.47 2.78
1215 5740 1.153745 AGCGCGTCTGAAGTCATCC 60.154 57.895 8.43 0.00 0.00 3.51
1292 5817 2.923121 TCATGAACTGCTCCAATAGGC 58.077 47.619 0.00 0.00 33.74 3.93
1450 5975 4.184629 GAGTCGAAGCAATCCATGTAGTT 58.815 43.478 0.00 0.00 0.00 2.24
1530 6055 3.452755 TCTACCATGTGGCAATAGACG 57.547 47.619 0.00 0.00 39.32 4.18
1578 6103 0.757935 GCCCGTGGGGTATCTGTCTA 60.758 60.000 7.14 0.00 46.51 2.59
1641 6166 1.703438 CCTCTCGGTCGTACACTCCG 61.703 65.000 12.23 12.23 44.76 4.63
1646 6171 0.325933 TCCTTCCTCTCGGTCGTACA 59.674 55.000 0.00 0.00 0.00 2.90
1650 6175 0.601558 TGTTTCCTTCCTCTCGGTCG 59.398 55.000 0.00 0.00 0.00 4.79
1665 6190 1.720694 CGTCGGCCACCACTTTGTTT 61.721 55.000 2.24 0.00 0.00 2.83
1824 6349 3.133003 TCGAGCCTTCAAGGAAAGGATAG 59.867 47.826 7.98 1.09 44.83 2.08
1852 6380 2.595238 AGTCGAGTGGGTGAACTACTT 58.405 47.619 0.00 0.00 0.00 2.24
1885 6413 7.841915 TCACATACTTCATAAAATCGAGCAA 57.158 32.000 0.00 0.00 0.00 3.91
1930 6461 0.740149 ATACAATGCACATGCCCGTG 59.260 50.000 0.49 0.00 41.18 4.94
1931 6462 1.024271 GATACAATGCACATGCCCGT 58.976 50.000 0.49 0.00 41.18 5.28
2015 6550 2.159254 ACAATGTTGTCACTGTTGGTGC 60.159 45.455 0.00 0.00 44.98 5.01
2085 6620 1.187715 CAACGACGCACCACTTTTTG 58.812 50.000 0.00 0.00 0.00 2.44
2086 6621 0.524604 GCAACGACGCACCACTTTTT 60.525 50.000 0.00 0.00 0.00 1.94
2087 6622 1.063488 GCAACGACGCACCACTTTT 59.937 52.632 0.00 0.00 0.00 2.27
2088 6623 2.713154 GCAACGACGCACCACTTT 59.287 55.556 0.00 0.00 0.00 2.66
2089 6624 3.276846 GGCAACGACGCACCACTT 61.277 61.111 0.00 0.00 0.00 3.16
2101 6636 1.864082 CAAATGAAACCAACCGGCAAC 59.136 47.619 0.00 0.00 34.57 4.17
2104 6639 0.676736 TCCAAATGAAACCAACCGGC 59.323 50.000 0.00 0.00 34.57 6.13
2121 6656 1.823976 GGAAGTCCCCTCGTCATCC 59.176 63.158 0.00 0.00 0.00 3.51
2148 6683 4.697514 TGCTGAAACCACTATCAGATAGC 58.302 43.478 16.35 3.53 44.64 2.97
2153 6688 2.676839 CAGCTGCTGAAACCACTATCAG 59.323 50.000 24.88 0.00 44.66 2.90
2154 6689 2.703416 CAGCTGCTGAAACCACTATCA 58.297 47.619 24.88 0.00 32.44 2.15
2155 6690 1.399791 GCAGCTGCTGAAACCACTATC 59.600 52.381 32.30 7.30 38.21 2.08
2160 6696 1.457823 CCTTGCAGCTGCTGAAACCA 61.458 55.000 36.61 17.61 42.66 3.67
2163 6699 2.567497 GCCCTTGCAGCTGCTGAAA 61.567 57.895 36.61 26.71 42.66 2.69
2191 6727 9.492973 CAATTAAAAGGAGATGTTTGGACAAAT 57.507 29.630 0.34 0.00 39.66 2.32
2197 6733 6.801862 GTCGTCAATTAAAAGGAGATGTTTGG 59.198 38.462 0.00 0.00 0.00 3.28
2198 6735 7.584987 AGTCGTCAATTAAAAGGAGATGTTTG 58.415 34.615 0.00 0.00 0.00 2.93
2202 6740 8.648557 TGATAGTCGTCAATTAAAAGGAGATG 57.351 34.615 0.00 0.00 0.00 2.90
2518 7096 0.107993 CGCTTGCCAGAGAGGATCAA 60.108 55.000 0.00 0.00 41.22 2.57
2521 7099 0.326264 AAACGCTTGCCAGAGAGGAT 59.674 50.000 0.00 0.00 41.22 3.24
2526 7104 1.133025 CCCAATAAACGCTTGCCAGAG 59.867 52.381 0.00 0.00 0.00 3.35
2527 7105 1.173043 CCCAATAAACGCTTGCCAGA 58.827 50.000 0.00 0.00 0.00 3.86
2529 7107 0.885196 GTCCCAATAAACGCTTGCCA 59.115 50.000 0.00 0.00 0.00 4.92
2530 7108 0.885196 TGTCCCAATAAACGCTTGCC 59.115 50.000 0.00 0.00 0.00 4.52
2533 7111 1.883926 GTGGTGTCCCAATAAACGCTT 59.116 47.619 0.00 0.00 44.15 4.68
2561 7140 2.307768 ACTAGATGTAGCAGCGCCTAA 58.692 47.619 2.29 0.00 0.00 2.69
2592 7171 0.315382 GCGCGTCAGCACAATACATC 60.315 55.000 8.43 0.00 45.49 3.06
2593 7172 1.705337 GGCGCGTCAGCACAATACAT 61.705 55.000 5.47 0.00 45.49 2.29
2594 7173 2.387445 GGCGCGTCAGCACAATACA 61.387 57.895 5.47 0.00 45.49 2.29
2595 7174 1.705337 ATGGCGCGTCAGCACAATAC 61.705 55.000 21.72 0.00 45.49 1.89
2597 7176 2.257286 GAATGGCGCGTCAGCACAAT 62.257 55.000 21.72 0.00 45.49 2.71
2600 7179 4.166011 GGAATGGCGCGTCAGCAC 62.166 66.667 21.72 12.63 45.49 4.40
2601 7180 4.695993 TGGAATGGCGCGTCAGCA 62.696 61.111 21.72 0.00 45.49 4.41
2602 7181 3.869272 CTGGAATGGCGCGTCAGC 61.869 66.667 21.72 13.92 40.74 4.26
2603 7182 2.572095 TACCTGGAATGGCGCGTCAG 62.572 60.000 21.72 6.70 0.00 3.51
2606 7185 2.186903 CTACCTGGAATGGCGCGT 59.813 61.111 8.43 0.00 0.00 6.01
2609 7188 0.035439 AACACCTACCTGGAATGGCG 60.035 55.000 0.00 0.00 39.71 5.69
2625 7204 1.371183 CTTCCCCTCGAGCACAACA 59.629 57.895 6.99 0.00 0.00 3.33
2627 7206 3.068881 CCTTCCCCTCGAGCACAA 58.931 61.111 6.99 0.00 0.00 3.33
2629 7208 3.254024 TTGCCTTCCCCTCGAGCAC 62.254 63.158 6.99 0.00 32.18 4.40
2638 8479 0.389025 CACCACTTTGTTGCCTTCCC 59.611 55.000 0.00 0.00 0.00 3.97
2658 8499 1.547820 GAGATCAGCATAGCCATCGGA 59.452 52.381 0.00 0.00 0.00 4.55
2663 8504 1.807755 GCAACGAGATCAGCATAGCCA 60.808 52.381 0.00 0.00 0.00 4.75
2671 8512 1.688735 TCCCATAGGCAACGAGATCAG 59.311 52.381 0.00 0.00 46.39 2.90
2678 8519 1.051812 AGATCCTCCCATAGGCAACG 58.948 55.000 0.00 0.00 46.10 4.10
2684 8525 2.039613 GGCCAGAAAGATCCTCCCATAG 59.960 54.545 0.00 0.00 0.00 2.23
2687 8528 0.549902 TGGCCAGAAAGATCCTCCCA 60.550 55.000 0.00 0.00 0.00 4.37
2705 8546 9.170734 TCAAATCTCTTAGTCAAATCTGGATTG 57.829 33.333 0.00 0.00 0.00 2.67
2718 8559 3.732471 GCGTCGAGCTCAAATCTCTTAGT 60.732 47.826 15.40 0.00 44.04 2.24
2720 8561 2.798680 GCGTCGAGCTCAAATCTCTTA 58.201 47.619 15.40 0.00 44.04 2.10
2739 8580 3.125316 CGGTCATACTTGTTCAAAGGAGC 59.875 47.826 0.00 0.00 0.00 4.70
2741 8582 3.071479 GCGGTCATACTTGTTCAAAGGA 58.929 45.455 0.00 0.00 0.00 3.36
2744 8585 3.628032 TGTTGCGGTCATACTTGTTCAAA 59.372 39.130 0.00 0.00 0.00 2.69
2756 8597 0.753867 TGTAGAAGGTGTTGCGGTCA 59.246 50.000 0.00 0.00 0.00 4.02
2768 8609 1.471119 TAGGGTCCTGCGTGTAGAAG 58.529 55.000 0.00 0.00 0.00 2.85
2780 8621 1.272769 GTGTAGCCGATGATAGGGTCC 59.727 57.143 0.00 0.00 40.37 4.46
2783 8624 2.239400 TCTGTGTAGCCGATGATAGGG 58.761 52.381 0.00 0.00 0.00 3.53
2784 8625 4.527509 AATCTGTGTAGCCGATGATAGG 57.472 45.455 0.00 0.00 0.00 2.57
2787 8628 4.774726 AGGATAATCTGTGTAGCCGATGAT 59.225 41.667 0.00 0.00 32.09 2.45
2792 8633 4.058817 GGAAAGGATAATCTGTGTAGCCG 58.941 47.826 0.00 0.00 32.09 5.52
2825 8666 2.939103 GCGGATGAACTACTCAGCATTT 59.061 45.455 0.00 0.00 42.55 2.32
2831 8672 2.826128 AGTTGAGCGGATGAACTACTCA 59.174 45.455 0.00 0.00 38.81 3.41


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

AutoCloner maintained by Alex Coulton.