Multiple sequence alignment - TraesCS1B01G098500

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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 TraesCS1B01G098500 chr1B 100.000 2537 0 0 1 2537 104905633 104903097 0.000000e+00 4686.0
1 TraesCS1B01G098500 chr1B 84.819 1627 222 10 933 2537 477473608 477471985 0.000000e+00 1613.0
2 TraesCS1B01G098500 chr1B 91.396 709 57 2 144 848 340592160 340592868 0.000000e+00 968.0
3 TraesCS1B01G098500 chr1B 96.053 76 1 1 838 913 455946934 455946861 3.430000e-24 122.0
4 TraesCS1B01G098500 chr7D 91.544 1632 115 9 924 2537 584318903 584320529 0.000000e+00 2228.0
5 TraesCS1B01G098500 chr7D 89.773 1633 145 9 922 2537 483944079 483945706 0.000000e+00 2071.0
6 TraesCS1B01G098500 chr7D 92.461 703 49 2 144 842 218405240 218405942 0.000000e+00 1002.0
7 TraesCS1B01G098500 chr7D 90.934 717 59 4 145 856 517602153 517601438 0.000000e+00 959.0
8 TraesCS1B01G098500 chr7D 100.000 65 0 0 849 913 126129276 126129212 1.230000e-23 121.0
9 TraesCS1B01G098500 chr6D 88.719 1631 156 10 924 2537 105116702 105115083 0.000000e+00 1967.0
10 TraesCS1B01G098500 chr6D 88.351 1631 156 14 924 2537 193427834 193429447 0.000000e+00 1929.0
11 TraesCS1B01G098500 chr6D 91.597 714 49 6 144 850 308148606 308149315 0.000000e+00 976.0
12 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 28769659 28769723 1.230000e-23 121.0
13 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 33766524 33766460 1.230000e-23 121.0
14 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 37977774 37977838 1.230000e-23 121.0
15 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 40695145 40695081 1.230000e-23 121.0
16 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 54955537 54955473 1.230000e-23 121.0
17 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 66941471 66941407 1.230000e-23 121.0
18 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 74040638 74040702 1.230000e-23 121.0
19 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 74105691 74105627 1.230000e-23 121.0
20 TraesCS1B01G098500 chr6D 100.000 65 0 0 849 913 74418824 74418888 1.230000e-23 121.0
21 TraesCS1B01G098500 chr5D 87.592 1636 179 11 920 2537 314526186 314527815 0.000000e+00 1875.0
22 TraesCS1B01G098500 chr2D 87.334 1658 153 23 923 2537 495060339 495061982 0.000000e+00 1845.0
23 TraesCS1B01G098500 chr2B 84.512 1569 216 14 932 2482 610750313 610751872 0.000000e+00 1526.0
24 TraesCS1B01G098500 chr2B 92.568 148 7 2 1 146 133201304 133201449 2.560000e-50 209.0
25 TraesCS1B01G098500 chr2B 100.000 67 0 0 847 913 180995030 180994964 9.530000e-25 124.0
26 TraesCS1B01G098500 chr4A 83.109 1634 246 18 923 2537 152833828 152832206 0.000000e+00 1461.0
27 TraesCS1B01G098500 chr7B 83.221 1633 229 27 933 2537 279632990 279631375 0.000000e+00 1456.0
28 TraesCS1B01G098500 chr7B 92.758 718 47 3 144 856 508146919 508146202 0.000000e+00 1033.0
29 TraesCS1B01G098500 chr7B 95.745 141 6 0 1 141 503074464 503074604 7.060000e-56 228.0
30 TraesCS1B01G098500 chr5B 83.407 1585 228 19 973 2537 184504104 184505673 0.000000e+00 1437.0
31 TraesCS1B01G098500 chr5B 94.326 141 7 1 1 141 422622591 422622730 5.500000e-52 215.0
32 TraesCS1B01G098500 chr3B 87.882 1114 131 4 1428 2537 786630076 786628963 0.000000e+00 1306.0
33 TraesCS1B01G098500 chr3B 90.329 517 33 2 923 1422 786642103 786641587 0.000000e+00 662.0
34 TraesCS1B01G098500 chr3B 92.958 142 9 1 1 141 407163891 407164032 3.310000e-49 206.0
35 TraesCS1B01G098500 chr3A 82.025 1274 195 16 938 2194 521840693 521839437 0.000000e+00 1053.0
36 TraesCS1B01G098500 chr4B 92.546 711 46 4 144 850 493598649 493597942 0.000000e+00 1013.0
37 TraesCS1B01G098500 chr4B 90.808 718 61 3 144 856 273643780 273643063 0.000000e+00 955.0
38 TraesCS1B01G098500 chr4B 98.529 68 1 0 846 913 48134360 48134427 1.230000e-23 121.0
39 TraesCS1B01G098500 chr4D 91.783 718 53 4 144 856 360011941 360012657 0.000000e+00 994.0
40 TraesCS1B01G098500 chr4D 75.253 198 43 6 999 1194 371722370 371722177 3.480000e-14 89.8
41 TraesCS1B01G098500 chr1D 86.268 852 106 7 15 856 390273423 390274273 0.000000e+00 915.0
42 TraesCS1B01G098500 chr1D 100.000 66 0 0 849 914 304929643 304929578 3.430000e-24 122.0
43 TraesCS1B01G098500 chr5A 95.000 140 6 1 1 139 106807465 106807604 4.250000e-53 219.0
44 TraesCS1B01G098500 chr6B 91.667 156 11 2 1 155 191674101 191673947 5.500000e-52 215.0
45 TraesCS1B01G098500 chr6B 100.000 67 0 0 847 913 53221261 53221327 9.530000e-25 124.0
46 TraesCS1B01G098500 chrUn 92.517 147 9 2 1 146 93295592 93295737 2.560000e-50 209.0
47 TraesCS1B01G098500 chr3D 93.056 144 8 2 2 144 525248718 525248860 2.560000e-50 209.0
48 TraesCS1B01G098500 chr3D 100.000 67 0 0 847 913 102975967 102976033 9.530000e-25 124.0
49 TraesCS1B01G098500 chr2A 100.000 67 0 0 847 913 664962178 664962244 9.530000e-25 124.0


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 TraesCS1B01G098500 chr1B 104903097 104905633 2536 True 4686 4686 100.000 1 2537 1 chr1B.!!$R1 2536
1 TraesCS1B01G098500 chr1B 477471985 477473608 1623 True 1613 1613 84.819 933 2537 1 chr1B.!!$R3 1604
2 TraesCS1B01G098500 chr1B 340592160 340592868 708 False 968 968 91.396 144 848 1 chr1B.!!$F1 704
3 TraesCS1B01G098500 chr7D 584318903 584320529 1626 False 2228 2228 91.544 924 2537 1 chr7D.!!$F3 1613
4 TraesCS1B01G098500 chr7D 483944079 483945706 1627 False 2071 2071 89.773 922 2537 1 chr7D.!!$F2 1615
5 TraesCS1B01G098500 chr7D 218405240 218405942 702 False 1002 1002 92.461 144 842 1 chr7D.!!$F1 698
6 TraesCS1B01G098500 chr7D 517601438 517602153 715 True 959 959 90.934 145 856 1 chr7D.!!$R2 711
7 TraesCS1B01G098500 chr6D 105115083 105116702 1619 True 1967 1967 88.719 924 2537 1 chr6D.!!$R6 1613
8 TraesCS1B01G098500 chr6D 193427834 193429447 1613 False 1929 1929 88.351 924 2537 1 chr6D.!!$F5 1613
9 TraesCS1B01G098500 chr6D 308148606 308149315 709 False 976 976 91.597 144 850 1 chr6D.!!$F6 706
10 TraesCS1B01G098500 chr5D 314526186 314527815 1629 False 1875 1875 87.592 920 2537 1 chr5D.!!$F1 1617
11 TraesCS1B01G098500 chr2D 495060339 495061982 1643 False 1845 1845 87.334 923 2537 1 chr2D.!!$F1 1614
12 TraesCS1B01G098500 chr2B 610750313 610751872 1559 False 1526 1526 84.512 932 2482 1 chr2B.!!$F2 1550
13 TraesCS1B01G098500 chr4A 152832206 152833828 1622 True 1461 1461 83.109 923 2537 1 chr4A.!!$R1 1614
14 TraesCS1B01G098500 chr7B 279631375 279632990 1615 True 1456 1456 83.221 933 2537 1 chr7B.!!$R1 1604
15 TraesCS1B01G098500 chr7B 508146202 508146919 717 True 1033 1033 92.758 144 856 1 chr7B.!!$R2 712
16 TraesCS1B01G098500 chr5B 184504104 184505673 1569 False 1437 1437 83.407 973 2537 1 chr5B.!!$F1 1564
17 TraesCS1B01G098500 chr3B 786628963 786630076 1113 True 1306 1306 87.882 1428 2537 1 chr3B.!!$R1 1109
18 TraesCS1B01G098500 chr3B 786641587 786642103 516 True 662 662 90.329 923 1422 1 chr3B.!!$R2 499
19 TraesCS1B01G098500 chr3A 521839437 521840693 1256 True 1053 1053 82.025 938 2194 1 chr3A.!!$R1 1256
20 TraesCS1B01G098500 chr4B 493597942 493598649 707 True 1013 1013 92.546 144 850 1 chr4B.!!$R2 706
21 TraesCS1B01G098500 chr4B 273643063 273643780 717 True 955 955 90.808 144 856 1 chr4B.!!$R1 712
22 TraesCS1B01G098500 chr4D 360011941 360012657 716 False 994 994 91.783 144 856 1 chr4D.!!$F1 712
23 TraesCS1B01G098500 chr1D 390273423 390274273 850 False 915 915 86.268 15 856 1 chr1D.!!$F1 841

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
81 82 0.179100 CCACACTCACTAGGCGATGG 60.179 60.0 0.00 0.0 0.0 3.51 F
1096 1112 0.318762 GGTGCACTTCTCTCCTTCGT 59.681 55.0 17.98 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1256 1272 0.768622 ATGTCCAACCTTGTTCCCGA 59.231 50.000 0.0 0.0 0.0 5.14 R
2457 2706 1.002134 ATGGCGAGGGAGTTGTTGG 60.002 57.895 0.0 0.0 0.0 3.77 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
17 18 4.874977 GTCAGTAGCCGCTCGCCC 62.875 72.222 0.00 0.00 38.78 6.13
34 35 1.449601 CCATCCCCGACGGTTTCTG 60.450 63.158 13.94 4.70 0.00 3.02
39 40 2.738480 CCGACGGTTTCTGGGTCA 59.262 61.111 5.48 0.00 0.00 4.02
62 63 2.517798 GGAAGGACCCCCTATCGCC 61.518 68.421 0.00 0.00 43.48 5.54
69 70 2.808206 CCCCCTATCGCCCACACTC 61.808 68.421 0.00 0.00 0.00 3.51
73 74 1.399714 CCTATCGCCCACACTCACTA 58.600 55.000 0.00 0.00 0.00 2.74
79 80 1.961180 GCCCACACTCACTAGGCGAT 61.961 60.000 0.00 0.00 33.18 4.58
81 82 0.179100 CCACACTCACTAGGCGATGG 60.179 60.000 0.00 0.00 0.00 3.51
85 86 0.824759 ACTCACTAGGCGATGGTTCC 59.175 55.000 0.00 0.00 0.00 3.62
93 94 1.603236 GGCGATGGTTCCAAATGCCA 61.603 55.000 19.88 0.00 40.66 4.92
97 98 0.461135 ATGGTTCCAAATGCCATCGC 59.539 50.000 0.00 0.00 38.52 4.58
98 99 0.611618 TGGTTCCAAATGCCATCGCT 60.612 50.000 0.00 0.00 35.36 4.93
130 131 6.294120 GGTTAAAAACCGTTTGTATAGCACCT 60.294 38.462 0.00 0.00 42.62 4.00
131 132 5.366829 AAAAACCGTTTGTATAGCACCTC 57.633 39.130 0.00 0.00 0.00 3.85
132 133 2.288961 ACCGTTTGTATAGCACCTCG 57.711 50.000 0.00 0.00 0.00 4.63
133 134 1.820519 ACCGTTTGTATAGCACCTCGA 59.179 47.619 0.00 0.00 0.00 4.04
136 137 3.444916 CGTTTGTATAGCACCTCGATGT 58.555 45.455 0.00 0.00 0.00 3.06
141 142 3.955551 TGTATAGCACCTCGATGTACCAA 59.044 43.478 0.00 0.00 0.00 3.67
265 270 1.203288 TCCCTCGGGGTAAAGTGGTTA 60.203 52.381 0.00 0.00 44.74 2.85
361 366 8.064336 AGCAATTCTCTTTGAGATTTAGCAAT 57.936 30.769 17.56 0.00 38.56 3.56
362 367 7.974501 AGCAATTCTCTTTGAGATTTAGCAATG 59.025 33.333 17.56 0.00 38.56 2.82
365 370 6.187125 TCTCTTTGAGATTTAGCAATGTGC 57.813 37.500 0.00 0.00 37.43 4.57
458 464 3.618594 GTCACTCAAGCGAGCAATCATAA 59.381 43.478 0.00 0.00 43.66 1.90
545 551 4.678509 TCAAACTCATAACGGCATTGAC 57.321 40.909 0.00 0.00 0.00 3.18
553 559 4.100963 TCATAACGGCATTGACTAGGATGT 59.899 41.667 0.00 0.00 0.00 3.06
554 560 3.350219 AACGGCATTGACTAGGATGTT 57.650 42.857 0.00 0.00 0.00 2.71
561 567 6.511767 CGGCATTGACTAGGATGTTTATTGTC 60.512 42.308 0.00 0.00 0.00 3.18
565 571 5.989477 TGACTAGGATGTTTATTGTCAGGG 58.011 41.667 0.00 0.00 0.00 4.45
566 572 5.724370 TGACTAGGATGTTTATTGTCAGGGA 59.276 40.000 0.00 0.00 0.00 4.20
572 578 7.227156 AGGATGTTTATTGTCAGGGATATCAC 58.773 38.462 4.83 0.00 0.00 3.06
573 579 6.431234 GGATGTTTATTGTCAGGGATATCACC 59.569 42.308 0.00 1.67 0.00 4.02
579 585 4.963318 TGTCAGGGATATCACCTTCATC 57.037 45.455 0.00 0.00 35.78 2.92
583 589 6.126390 TGTCAGGGATATCACCTTCATCAAAT 60.126 38.462 0.00 0.00 35.78 2.32
587 593 6.779539 AGGGATATCACCTTCATCAAATTTCC 59.220 38.462 0.00 0.00 33.64 3.13
589 595 7.040132 GGGATATCACCTTCATCAAATTTCCTC 60.040 40.741 4.83 0.00 0.00 3.71
591 597 8.827832 ATATCACCTTCATCAAATTTCCTCAA 57.172 30.769 0.00 0.00 0.00 3.02
595 601 7.040201 TCACCTTCATCAAATTTCCTCAAAGAG 60.040 37.037 0.00 0.00 0.00 2.85
625 637 3.395630 ACCGGTGGTGGTGTATCC 58.604 61.111 6.12 0.00 41.85 2.59
708 720 5.964958 TCCTTCATACTTTTCTTTGCCTG 57.035 39.130 0.00 0.00 0.00 4.85
712 724 4.870363 TCATACTTTTCTTTGCCTGTTGC 58.130 39.130 0.00 0.00 41.77 4.17
727 739 3.875727 CCTGTTGCATATCTTCAGGACTG 59.124 47.826 3.76 0.00 45.76 3.51
736 748 8.747471 TGCATATCTTCAGGACTGAGATATAAG 58.253 37.037 20.84 15.49 41.13 1.73
753 765 6.893005 AGATATAAGATACCCCTCTTCTTCGG 59.107 42.308 0.00 0.00 36.82 4.30
757 769 3.462579 AGATACCCCTCTTCTTCGGAGTA 59.537 47.826 0.00 0.00 0.00 2.59
768 780 1.747355 CTTCGGAGTAGGTTTAGGCGA 59.253 52.381 0.00 0.00 0.00 5.54
780 792 2.678336 GTTTAGGCGATGGTTCAGGAAG 59.322 50.000 0.00 0.00 0.00 3.46
781 793 1.860641 TAGGCGATGGTTCAGGAAGA 58.139 50.000 0.00 0.00 0.00 2.87
832 844 8.579850 TGTTATTCAATAATTCCTCAGCTTGT 57.420 30.769 0.00 0.00 0.00 3.16
833 845 9.023962 TGTTATTCAATAATTCCTCAGCTTGTT 57.976 29.630 0.00 0.00 0.00 2.83
843 855 5.227569 TCCTCAGCTTGTTCAATAGTTCA 57.772 39.130 0.00 0.00 0.00 3.18
850 862 6.599244 CAGCTTGTTCAATAGTTCATTCCCTA 59.401 38.462 0.00 0.00 0.00 3.53
852 864 7.121315 AGCTTGTTCAATAGTTCATTCCCTAAC 59.879 37.037 0.00 0.00 0.00 2.34
854 866 7.681939 TGTTCAATAGTTCATTCCCTAACAC 57.318 36.000 0.00 0.00 0.00 3.32
855 867 7.227873 TGTTCAATAGTTCATTCCCTAACACA 58.772 34.615 0.00 0.00 0.00 3.72
857 869 8.739972 GTTCAATAGTTCATTCCCTAACACAAT 58.260 33.333 0.00 0.00 0.00 2.71
858 870 9.967451 TTCAATAGTTCATTCCCTAACACAATA 57.033 29.630 0.00 0.00 0.00 1.90
859 871 9.967451 TCAATAGTTCATTCCCTAACACAATAA 57.033 29.630 0.00 0.00 0.00 1.40
863 875 8.877864 AGTTCATTCCCTAACACAATAAATCA 57.122 30.769 0.00 0.00 0.00 2.57
864 876 9.479549 AGTTCATTCCCTAACACAATAAATCAT 57.520 29.630 0.00 0.00 0.00 2.45
969 985 1.306141 CTCCCACCTGCTCCACCTA 60.306 63.158 0.00 0.00 0.00 3.08
1042 1058 0.471591 TTTCAACCCTGGCCTTGCAT 60.472 50.000 3.32 0.00 0.00 3.96
1096 1112 0.318762 GGTGCACTTCTCTCCTTCGT 59.681 55.000 17.98 0.00 0.00 3.85
1256 1272 1.947456 GTCCTTTCGCTTTTCTGTGGT 59.053 47.619 0.00 0.00 0.00 4.16
1301 1317 1.490490 TCATGGCCTCAAGGACCATAC 59.510 52.381 18.58 0.00 44.80 2.39
1336 1365 4.452114 TCATCTGTTCAATGGTCGTTTCAG 59.548 41.667 0.00 0.00 0.00 3.02
1674 1710 6.780457 ACTCCAGATTGGTAATTTCCATTG 57.220 37.500 4.46 4.61 39.03 2.82
1700 1736 5.009010 CCATGCAATATCACTTACCCTCAAC 59.991 44.000 0.00 0.00 0.00 3.18
1704 1740 6.156256 TGCAATATCACTTACCCTCAACTACT 59.844 38.462 0.00 0.00 0.00 2.57
1789 1826 1.798223 CCACGGCACATATTACGGATG 59.202 52.381 0.00 0.00 0.00 3.51
1803 1840 1.594293 GGATGTATCACGTGCGGGG 60.594 63.158 11.67 0.00 0.00 5.73
1804 1841 1.440060 GATGTATCACGTGCGGGGA 59.560 57.895 11.67 0.00 0.00 4.81
1844 1881 5.782331 TGATTGATTTGGTTAATGGTTGGGA 59.218 36.000 0.00 0.00 0.00 4.37
1845 1882 6.270927 TGATTGATTTGGTTAATGGTTGGGAA 59.729 34.615 0.00 0.00 0.00 3.97
1872 1909 5.301551 TCTCTGTGCCAAATGTTTACAATGT 59.698 36.000 0.00 0.00 0.00 2.71
1873 1910 5.911752 TCTGTGCCAAATGTTTACAATGTT 58.088 33.333 0.00 0.00 0.00 2.71
1880 1918 6.293298 GCCAAATGTTTACAATGTTGCATGAA 60.293 34.615 0.00 0.00 0.00 2.57
1895 1933 5.423704 TGCATGAAAAATCCCATTGTCAT 57.576 34.783 0.00 0.00 31.59 3.06
2031 2069 7.872113 AATTCAGTCAAATCTTATCACCCTC 57.128 36.000 0.00 0.00 0.00 4.30
2037 2075 5.068723 GTCAAATCTTATCACCCTCGGTAGA 59.931 44.000 0.00 0.00 32.11 2.59
2050 2088 4.160626 CCCTCGGTAGAAAATCAACTCTCT 59.839 45.833 0.00 0.00 0.00 3.10
2152 2190 1.066430 TGGACACCTGGCGTAATCTTC 60.066 52.381 0.00 0.00 0.00 2.87
2158 2196 1.412710 CCTGGCGTAATCTTCCTAGCA 59.587 52.381 0.00 0.00 0.00 3.49
2307 2517 2.830827 CACCACAAACCACCGCCA 60.831 61.111 0.00 0.00 0.00 5.69
2308 2518 2.831284 ACCACAAACCACCGCCAC 60.831 61.111 0.00 0.00 0.00 5.01
2309 2519 3.601685 CCACAAACCACCGCCACC 61.602 66.667 0.00 0.00 0.00 4.61
2313 2523 4.130554 AAACCACCGCCACCACCA 62.131 61.111 0.00 0.00 0.00 4.17
2398 2646 1.302285 CTGGCTGGTCCATTGAGCT 59.698 57.895 0.00 0.00 45.50 4.09
2466 2715 1.966451 CGCCCCTCACCAACAACTC 60.966 63.158 0.00 0.00 0.00 3.01
2487 2736 0.872021 CTCGCCATCACCGAAGCTAC 60.872 60.000 0.00 0.00 33.92 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.227134 ATGGGCGAGCGGCTACTG 62.227 66.667 15.91 0.00 42.94 2.74
3 4 3.917760 GATGGGCGAGCGGCTACT 61.918 66.667 15.91 1.48 42.94 2.57
17 18 1.449601 CCAGAAACCGTCGGGGATG 60.450 63.158 17.28 8.50 37.90 3.51
22 23 1.019278 CATGACCCAGAAACCGTCGG 61.019 60.000 10.48 10.48 0.00 4.79
28 29 2.162681 CTTCCCACATGACCCAGAAAC 58.837 52.381 0.00 0.00 0.00 2.78
34 35 1.303282 GGTCCTTCCCACATGACCC 59.697 63.158 0.00 0.00 41.14 4.46
52 53 2.063979 TGAGTGTGGGCGATAGGGG 61.064 63.158 0.00 0.00 0.00 4.79
62 63 0.179100 CCATCGCCTAGTGAGTGTGG 60.179 60.000 0.00 0.00 0.00 4.17
69 70 2.107950 TTTGGAACCATCGCCTAGTG 57.892 50.000 0.00 0.00 0.00 2.74
73 74 1.322538 GGCATTTGGAACCATCGCCT 61.323 55.000 16.27 0.00 34.27 5.52
79 80 0.611618 AGCGATGGCATTTGGAACCA 60.612 50.000 0.00 0.00 43.41 3.67
81 82 0.810648 TCAGCGATGGCATTTGGAAC 59.189 50.000 0.00 0.00 43.41 3.62
85 86 1.470285 CCCTTTCAGCGATGGCATTTG 60.470 52.381 0.00 1.27 43.41 2.32
93 94 3.257375 GGTTTTTAACCCCTTTCAGCGAT 59.743 43.478 0.00 0.00 46.12 4.58
122 123 3.244215 CCATTGGTACATCGAGGTGCTAT 60.244 47.826 17.47 8.99 39.30 2.97
126 127 2.691409 ACCATTGGTACATCGAGGTG 57.309 50.000 13.92 0.00 39.30 4.00
130 131 3.828875 TGCATACCATTGGTACATCGA 57.171 42.857 17.71 0.00 41.31 3.59
131 132 4.335315 ACTTTGCATACCATTGGTACATCG 59.665 41.667 17.71 8.10 41.31 3.84
132 133 5.221048 GGACTTTGCATACCATTGGTACATC 60.221 44.000 17.71 10.08 41.31 3.06
133 134 4.644685 GGACTTTGCATACCATTGGTACAT 59.355 41.667 17.71 1.29 41.31 2.29
136 137 4.584638 AGGACTTTGCATACCATTGGTA 57.415 40.909 17.67 17.67 42.80 3.25
141 142 7.902920 AAAATGATAGGACTTTGCATACCAT 57.097 32.000 0.00 0.00 0.00 3.55
183 188 4.946478 ATGATGCACCTAGTCCTTCTAC 57.054 45.455 0.00 0.00 0.00 2.59
224 229 5.480422 GGGACACCCTAAAAGAATTGAACAT 59.520 40.000 0.00 0.00 41.34 2.71
254 259 8.501580 GGTAAAATGACTCAGTAACCACTTTAC 58.498 37.037 2.12 2.12 40.57 2.01
265 270 6.257586 ACTAGAGGAGGTAAAATGACTCAGT 58.742 40.000 0.00 0.00 32.98 3.41
365 370 9.285153 GCCTCTATGGTTCAGACTCAACTAGAG 62.285 48.148 7.95 7.95 43.48 2.43
377 382 4.096984 GGAAAACATGCCTCTATGGTTCAG 59.903 45.833 0.00 0.00 36.99 3.02
523 529 4.943705 AGTCAATGCCGTTATGAGTTTGAT 59.056 37.500 0.00 0.00 0.00 2.57
545 551 8.597167 TGATATCCCTGACAATAAACATCCTAG 58.403 37.037 0.00 0.00 0.00 3.02
553 559 7.206789 TGAAGGTGATATCCCTGACAATAAA 57.793 36.000 12.03 0.00 30.99 1.40
554 560 6.823286 TGAAGGTGATATCCCTGACAATAA 57.177 37.500 12.03 0.00 30.99 1.40
561 567 7.255730 GGAAATTTGATGAAGGTGATATCCCTG 60.256 40.741 12.03 0.00 30.99 4.45
565 571 8.455903 TGAGGAAATTTGATGAAGGTGATATC 57.544 34.615 0.00 0.00 0.00 1.63
566 572 8.827832 TTGAGGAAATTTGATGAAGGTGATAT 57.172 30.769 0.00 0.00 0.00 1.63
572 578 7.224522 ACTCTTTGAGGAAATTTGATGAAGG 57.775 36.000 0.00 0.00 33.35 3.46
595 601 1.066645 CCACCGGTGGTAGAGGTAAAC 60.067 57.143 40.44 0.00 45.53 2.01
611 617 1.077716 GGCTGGATACACCACCACC 60.078 63.158 0.00 0.00 46.17 4.61
624 636 5.242393 CCTATTGAAGAAATACATGGGCTGG 59.758 44.000 0.00 0.00 0.00 4.85
625 637 6.064060 TCCTATTGAAGAAATACATGGGCTG 58.936 40.000 0.00 0.00 0.00 4.85
661 673 9.860898 GAAAAATGTATTAAAGCAGAGGATGTT 57.139 29.630 0.00 0.00 0.00 2.71
681 693 8.432013 AGGCAAAGAAAAGTATGAAGGAAAAAT 58.568 29.630 0.00 0.00 0.00 1.82
682 694 7.710475 CAGGCAAAGAAAAGTATGAAGGAAAAA 59.290 33.333 0.00 0.00 0.00 1.94
708 720 5.016051 TCTCAGTCCTGAAGATATGCAAC 57.984 43.478 0.00 0.00 39.39 4.17
727 739 7.067737 CCGAAGAAGAGGGGTATCTTATATCTC 59.932 44.444 0.00 0.00 39.63 2.75
736 748 2.668625 ACTCCGAAGAAGAGGGGTATC 58.331 52.381 0.00 0.00 0.00 2.24
738 750 2.091994 CCTACTCCGAAGAAGAGGGGTA 60.092 54.545 0.00 0.00 0.00 3.69
753 765 3.118884 TGAACCATCGCCTAAACCTACTC 60.119 47.826 0.00 0.00 0.00 2.59
757 769 1.065418 CCTGAACCATCGCCTAAACCT 60.065 52.381 0.00 0.00 0.00 3.50
768 780 3.588842 TGATTGGACTCTTCCTGAACCAT 59.411 43.478 0.00 0.00 43.31 3.55
816 828 8.814038 AACTATTGAACAAGCTGAGGAATTAT 57.186 30.769 0.00 0.00 0.00 1.28
823 835 6.404074 GGGAATGAACTATTGAACAAGCTGAG 60.404 42.308 0.00 0.00 0.00 3.35
832 844 8.877864 ATTGTGTTAGGGAATGAACTATTGAA 57.122 30.769 0.00 0.00 0.00 2.69
833 845 9.967451 TTATTGTGTTAGGGAATGAACTATTGA 57.033 29.630 0.00 0.00 0.00 2.57
899 911 9.790344 CATCATTCTCCTCCTGAATAATTAAGT 57.210 33.333 0.00 0.00 33.38 2.24
900 912 9.228949 CCATCATTCTCCTCCTGAATAATTAAG 57.771 37.037 0.00 0.00 33.38 1.85
901 913 7.667219 GCCATCATTCTCCTCCTGAATAATTAA 59.333 37.037 0.00 0.00 33.38 1.40
902 914 7.170965 GCCATCATTCTCCTCCTGAATAATTA 58.829 38.462 0.00 0.00 33.38 1.40
903 915 6.008960 GCCATCATTCTCCTCCTGAATAATT 58.991 40.000 0.00 0.00 33.38 1.40
904 916 5.568392 GCCATCATTCTCCTCCTGAATAAT 58.432 41.667 0.00 0.00 33.38 1.28
905 917 4.503817 CGCCATCATTCTCCTCCTGAATAA 60.504 45.833 0.00 0.00 33.38 1.40
906 918 3.007290 CGCCATCATTCTCCTCCTGAATA 59.993 47.826 0.00 0.00 33.38 1.75
907 919 2.224475 CGCCATCATTCTCCTCCTGAAT 60.224 50.000 0.00 0.00 34.82 2.57
908 920 1.139654 CGCCATCATTCTCCTCCTGAA 59.860 52.381 0.00 0.00 0.00 3.02
909 921 0.755079 CGCCATCATTCTCCTCCTGA 59.245 55.000 0.00 0.00 0.00 3.86
910 922 0.883814 GCGCCATCATTCTCCTCCTG 60.884 60.000 0.00 0.00 0.00 3.86
911 923 1.449353 GCGCCATCATTCTCCTCCT 59.551 57.895 0.00 0.00 0.00 3.69
912 924 1.599240 GGCGCCATCATTCTCCTCC 60.599 63.158 24.80 0.00 0.00 4.30
913 925 1.958205 CGGCGCCATCATTCTCCTC 60.958 63.158 28.98 0.00 0.00 3.71
914 926 2.109799 CGGCGCCATCATTCTCCT 59.890 61.111 28.98 0.00 0.00 3.69
915 927 3.654020 GCGGCGCCATCATTCTCC 61.654 66.667 28.98 0.00 0.00 3.71
916 928 2.590007 AGCGGCGCCATCATTCTC 60.590 61.111 30.40 4.10 0.00 2.87
917 929 2.590007 GAGCGGCGCCATCATTCT 60.590 61.111 30.40 12.40 0.00 2.40
918 930 3.654020 GGAGCGGCGCCATCATTC 61.654 66.667 30.40 18.13 0.00 2.67
919 931 4.181010 AGGAGCGGCGCCATCATT 62.181 61.111 30.40 8.89 0.00 2.57
920 932 4.615815 GAGGAGCGGCGCCATCAT 62.616 66.667 30.40 21.39 0.00 2.45
969 985 7.192852 GATCATAGGTTAGATCCATGGTGAT 57.807 40.000 12.58 9.16 35.69 3.06
1042 1058 3.291101 GACGTACCTGCTCGGCCAA 62.291 63.158 2.24 0.00 35.61 4.52
1096 1112 5.358922 CAAGAAAAATTCCTTGGTCTTGCA 58.641 37.500 0.00 0.00 35.13 4.08
1235 1251 2.222027 CCACAGAAAAGCGAAAGGACT 58.778 47.619 0.00 0.00 0.00 3.85
1256 1272 0.768622 ATGTCCAACCTTGTTCCCGA 59.231 50.000 0.00 0.00 0.00 5.14
1336 1365 3.763897 AGAATCCAAATGCTTGTACCCAC 59.236 43.478 0.00 0.00 0.00 4.61
1607 1643 1.131126 GCATTGAATGACCGTGTCTGG 59.869 52.381 9.76 0.00 33.15 3.86
1674 1710 4.718961 AGGGTAAGTGATATTGCATGGAC 58.281 43.478 0.00 0.00 0.00 4.02
1789 1826 1.779569 CTATTCCCCGCACGTGATAC 58.220 55.000 22.23 0.00 0.00 2.24
1844 1881 5.359576 TGTAAACATTTGGCACAGAGAACTT 59.640 36.000 0.00 0.00 42.39 2.66
1845 1882 4.887071 TGTAAACATTTGGCACAGAGAACT 59.113 37.500 0.00 0.00 42.39 3.01
1872 1909 5.224821 TGACAATGGGATTTTTCATGCAA 57.775 34.783 0.00 0.00 0.00 4.08
1873 1910 4.886496 TGACAATGGGATTTTTCATGCA 57.114 36.364 0.00 0.00 0.00 3.96
1880 1918 1.481772 CGGGCATGACAATGGGATTTT 59.518 47.619 0.00 0.00 34.09 1.82
1895 1933 1.340502 TGCAGACAAATAATCCGGGCA 60.341 47.619 0.00 0.00 0.00 5.36
2021 2059 5.943349 TGATTTTCTACCGAGGGTGATAA 57.057 39.130 0.00 0.00 36.19 1.75
2031 2069 7.062371 CACAGTTAGAGAGTTGATTTTCTACCG 59.938 40.741 0.00 0.00 0.00 4.02
2037 2075 8.506168 TGTTTCACAGTTAGAGAGTTGATTTT 57.494 30.769 0.00 0.00 0.00 1.82
2050 2088 8.570068 AGAAAGTTAGGTTTGTTTCACAGTTA 57.430 30.769 0.00 0.00 32.38 2.24
2066 2104 3.243002 CCCTAGGCGTCGTAGAAAGTTAG 60.243 52.174 2.05 0.00 39.69 2.34
2069 2107 1.101331 CCCTAGGCGTCGTAGAAAGT 58.899 55.000 2.05 0.00 39.69 2.66
2118 2156 2.159014 GGTGTCCATAGTGACCGCATAA 60.159 50.000 0.00 0.00 34.25 1.90
2188 2226 1.860906 TGGTAGAGGGGGTTTTTGGTT 59.139 47.619 0.00 0.00 0.00 3.67
2307 2517 2.911143 GGAGATGGCGATGGTGGT 59.089 61.111 0.00 0.00 0.00 4.16
2308 2518 2.280389 CGGAGATGGCGATGGTGG 60.280 66.667 0.00 0.00 0.00 4.61
2309 2519 2.969238 GCGGAGATGGCGATGGTG 60.969 66.667 0.00 0.00 0.00 4.17
2457 2706 1.002134 ATGGCGAGGGAGTTGTTGG 60.002 57.895 0.00 0.00 0.00 3.77
2466 2715 2.202932 CTTCGGTGATGGCGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
2487 2736 3.451894 GCAGGGGCACAAATCGGG 61.452 66.667 0.00 0.00 40.72 5.14


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

AutoCloner maintained by Alex Coulton.