Multiple sequence alignment - TraesCS3B01G060700

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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 TraesCS3B01G060700 chr3B 100.000 2396 0 0 1 2396 32597728 32595333 0.000000e+00 4425.0
1 TraesCS3B01G060700 chr3B 98.633 2195 11 4 202 2396 32540378 32538203 0.000000e+00 3869.0
2 TraesCS3B01G060700 chr3B 88.051 1247 48 37 202 1404 32462990 32461801 0.000000e+00 1384.0
3 TraesCS3B01G060700 chr3B 88.154 726 48 9 205 911 32467164 32466458 0.000000e+00 830.0
4 TraesCS3B01G060700 chr3B 87.603 726 52 9 205 911 32544538 32543832 0.000000e+00 808.0
5 TraesCS3B01G060700 chr3B 86.328 768 55 25 1667 2396 32498658 32497903 0.000000e+00 791.0
6 TraesCS3B01G060700 chr3B 85.677 768 60 25 1667 2396 32567569 32566814 0.000000e+00 763.0
7 TraesCS3B01G060700 chr3B 89.134 543 48 7 1753 2290 32461100 32460564 0.000000e+00 665.0
8 TraesCS3B01G060700 chr3B 92.478 226 13 3 1529 1752 32461414 32461191 1.070000e-83 320.0
9 TraesCS3B01G060700 chr3B 78.272 405 58 16 920 1307 32712866 32712475 1.430000e-57 233.0
10 TraesCS3B01G060700 chr3B 86.957 184 16 5 1449 1630 32499976 32499799 1.450000e-47 200.0
11 TraesCS3B01G060700 chr3B 86.957 184 16 5 1449 1630 32507860 32507683 1.450000e-47 200.0
12 TraesCS3B01G060700 chr3B 86.957 184 16 5 1449 1630 32511878 32511701 1.450000e-47 200.0
13 TraesCS3B01G060700 chr3B 86.957 184 16 5 1449 1630 32568886 32568709 1.450000e-47 200.0
14 TraesCS3B01G060700 chr3B 97.273 110 3 0 947 1056 32466458 32466349 1.130000e-43 187.0
15 TraesCS3B01G060700 chr3B 97.273 110 3 0 947 1056 32543832 32543723 1.130000e-43 187.0
16 TraesCS3B01G060700 chr3B 77.316 313 49 14 941 1240 32726233 32725930 5.300000e-37 165.0
17 TraesCS3B01G060700 chr3B 76.632 291 54 8 1633 1920 32937739 32937460 5.340000e-32 148.0
18 TraesCS3B01G060700 chr3B 84.177 158 16 7 1431 1580 32461568 32461412 6.900000e-31 145.0
19 TraesCS3B01G060700 chr3B 98.667 75 1 0 1 75 492986674 492986600 1.490000e-27 134.0
20 TraesCS3B01G060700 chr3B 96.203 79 3 0 1 79 2385527 2385605 1.930000e-26 130.0
21 TraesCS3B01G060700 chr3B 93.182 88 5 1 1 87 489795571 489795484 6.950000e-26 128.0
22 TraesCS3B01G060700 chr3B 89.247 93 10 0 630 722 32713399 32713307 1.500000e-22 117.0
23 TraesCS3B01G060700 chr3B 92.593 81 5 1 76 156 32463070 32462991 5.410000e-22 115.0
24 TraesCS3B01G060700 chr3B 83.065 124 19 2 1749 1871 32732261 32732139 7.000000e-21 111.0
25 TraesCS3B01G060700 chr3B 90.244 41 3 1 2329 2368 32460512 32460472 4.000000e-03 52.8
26 TraesCS3B01G060700 chr3A 86.947 881 82 20 1431 2290 27765829 27764961 0.000000e+00 959.0
27 TraesCS3B01G060700 chr3A 78.627 641 61 49 799 1406 27798517 27797920 2.930000e-94 355.0
28 TraesCS3B01G060700 chr3A 77.100 607 67 36 698 1282 27766733 27766177 3.900000e-73 285.0
29 TraesCS3B01G060700 chr3D 85.602 889 85 23 1431 2290 20017343 20016469 0.000000e+00 893.0
30 TraesCS3B01G060700 chr3D 85.558 824 81 19 1521 2323 20088380 20087574 0.000000e+00 828.0
31 TraesCS3B01G060700 chr3D 81.615 582 65 21 1632 2195 20158669 20158112 6.080000e-121 444.0
32 TraesCS3B01G060700 chr3D 79.839 620 53 33 682 1282 20041190 20040624 1.040000e-103 387.0
33 TraesCS3B01G060700 chr3D 79.002 581 69 34 729 1282 20142525 20141971 4.900000e-92 348.0
34 TraesCS3B01G060700 chr3D 82.210 371 43 10 580 944 20106745 20106392 5.010000e-77 298.0
35 TraesCS3B01G060700 chr3D 95.000 40 1 1 2329 2367 20087542 20087503 7.150000e-06 62.1
36 TraesCS3B01G060700 chr3D 90.244 41 3 1 2329 2368 20016417 20016377 4.000000e-03 52.8
37 TraesCS3B01G060700 chrUn 88.414 561 40 16 1667 2214 470183911 470183363 0.000000e+00 652.0
38 TraesCS3B01G060700 chrUn 89.409 406 27 3 335 739 479250690 479251080 4.600000e-137 497.0
39 TraesCS3B01G060700 chr7B 98.667 75 1 0 1 75 543439110 543439184 1.490000e-27 134.0
40 TraesCS3B01G060700 chr7B 89.130 92 5 4 118 207 430307326 430307414 2.520000e-20 110.0
41 TraesCS3B01G060700 chr5B 97.436 78 2 0 1 78 278664721 278664644 1.490000e-27 134.0
42 TraesCS3B01G060700 chr5B 89.130 92 5 4 118 207 107375968 107376056 2.520000e-20 110.0
43 TraesCS3B01G060700 chr5B 92.754 69 4 1 2329 2396 652226869 652226801 5.450000e-17 99.0
44 TraesCS3B01G060700 chr2B 94.186 86 5 0 1 86 601231184 601231269 5.370000e-27 132.0
45 TraesCS3B01G060700 chr2B 87.000 100 7 5 115 210 222220230 222220327 9.060000e-20 108.0
46 TraesCS3B01G060700 chr6B 95.122 82 4 0 1 82 647397026 647397107 1.930000e-26 130.0
47 TraesCS3B01G060700 chr6B 85.156 128 17 2 84 209 714919856 714919729 1.930000e-26 130.0
48 TraesCS3B01G060700 chr6B 93.023 86 2 4 128 211 114032404 114032487 3.230000e-24 122.0
49 TraesCS3B01G060700 chr1D 96.203 79 3 0 1 79 10232154 10232076 1.930000e-26 130.0
50 TraesCS3B01G060700 chr1B 95.062 81 4 0 1 81 386411924 386411844 6.950000e-26 128.0
51 TraesCS3B01G060700 chr4B 85.156 128 13 4 84 206 647731116 647731242 2.500000e-25 126.0
52 TraesCS3B01G060700 chr2A 88.235 102 7 4 108 207 761432959 761433057 1.500000e-22 117.0
53 TraesCS3B01G060700 chr5D 92.593 81 3 3 128 206 208140922 208140843 1.950000e-21 113.0
54 TraesCS3B01G060700 chr7D 89.011 91 7 2 120 208 246403472 246403383 2.520000e-20 110.0


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 TraesCS3B01G060700 chr3B 32595333 32597728 2395 True 4425.000000 4425 100.0000 1 2396 1 chr3B.!!$R1 2395
1 TraesCS3B01G060700 chr3B 32538203 32544538 6335 True 1621.333333 3869 94.5030 202 2396 3 chr3B.!!$R10 2194
2 TraesCS3B01G060700 chr3B 32497903 32499976 2073 True 495.500000 791 86.6425 1449 2396 2 chr3B.!!$R8 947
3 TraesCS3B01G060700 chr3B 32566814 32568886 2072 True 481.500000 763 86.3170 1449 2396 2 chr3B.!!$R11 947
4 TraesCS3B01G060700 chr3B 32460472 32467164 6692 True 462.350000 1384 90.2630 76 2368 8 chr3B.!!$R7 2292
5 TraesCS3B01G060700 chr3A 27764961 27766733 1772 True 622.000000 959 82.0235 698 2290 2 chr3A.!!$R2 1592
6 TraesCS3B01G060700 chr3A 27797920 27798517 597 True 355.000000 355 78.6270 799 1406 1 chr3A.!!$R1 607
7 TraesCS3B01G060700 chr3D 20016377 20017343 966 True 472.900000 893 87.9230 1431 2368 2 chr3D.!!$R5 937
8 TraesCS3B01G060700 chr3D 20087503 20088380 877 True 445.050000 828 90.2790 1521 2367 2 chr3D.!!$R6 846
9 TraesCS3B01G060700 chr3D 20158112 20158669 557 True 444.000000 444 81.6150 1632 2195 1 chr3D.!!$R4 563
10 TraesCS3B01G060700 chr3D 20040624 20041190 566 True 387.000000 387 79.8390 682 1282 1 chr3D.!!$R1 600
11 TraesCS3B01G060700 chr3D 20141971 20142525 554 True 348.000000 348 79.0020 729 1282 1 chr3D.!!$R3 553
12 TraesCS3B01G060700 chrUn 470183363 470183911 548 True 652.000000 652 88.4140 1667 2214 1 chrUn.!!$R1 547

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
99 100 0.108207 TTTTACTCCCGCCGTTCCAA 59.892 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 7671 3.258372 TCCAAGATAGAGCGAGTTGTTGT 59.742 43.478 0.0 0.0 0.0 3.32 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
38 39 7.894753 TGAAAGTGAATAATATTGGCATGGA 57.105 32.000 0.00 0.00 0.00 3.41
39 40 8.303780 TGAAAGTGAATAATATTGGCATGGAA 57.696 30.769 0.00 0.00 0.00 3.53
60 61 7.680982 TGGAACAATCGAAAATTACAGATACG 58.319 34.615 0.00 0.00 31.92 3.06
61 62 7.546316 TGGAACAATCGAAAATTACAGATACGA 59.454 33.333 0.00 0.00 31.92 3.43
62 63 7.844653 GGAACAATCGAAAATTACAGATACGAC 59.155 37.037 0.00 0.00 0.00 4.34
63 64 6.919188 ACAATCGAAAATTACAGATACGACG 58.081 36.000 0.00 0.00 0.00 5.12
65 66 5.233957 TCGAAAATTACAGATACGACGGA 57.766 39.130 0.00 0.00 0.00 4.69
66 67 5.268544 TCGAAAATTACAGATACGACGGAG 58.731 41.667 0.00 0.00 0.00 4.63
67 68 5.065090 TCGAAAATTACAGATACGACGGAGA 59.935 40.000 0.00 0.00 0.00 3.71
68 69 5.170981 CGAAAATTACAGATACGACGGAGAC 59.829 44.000 0.00 0.00 0.00 3.36
85 86 5.405331 GGAGACGTATCATTGCCTTTTAC 57.595 43.478 12.92 0.00 0.00 2.01
87 88 5.234543 GGAGACGTATCATTGCCTTTTACTC 59.765 44.000 12.92 0.00 0.00 2.59
90 91 3.247648 CGTATCATTGCCTTTTACTCCCG 59.752 47.826 0.00 0.00 0.00 5.14
91 92 1.459450 TCATTGCCTTTTACTCCCGC 58.541 50.000 0.00 0.00 0.00 6.13
92 93 0.455815 CATTGCCTTTTACTCCCGCC 59.544 55.000 0.00 0.00 0.00 6.13
93 94 1.029947 ATTGCCTTTTACTCCCGCCG 61.030 55.000 0.00 0.00 0.00 6.46
94 95 2.046604 GCCTTTTACTCCCGCCGT 60.047 61.111 0.00 0.00 0.00 5.68
95 96 1.673337 GCCTTTTACTCCCGCCGTT 60.673 57.895 0.00 0.00 0.00 4.44
99 100 0.108207 TTTTACTCCCGCCGTTCCAA 59.892 50.000 0.00 0.00 0.00 3.53
100 101 0.108207 TTTACTCCCGCCGTTCCAAA 59.892 50.000 0.00 0.00 0.00 3.28
101 102 0.108207 TTACTCCCGCCGTTCCAAAA 59.892 50.000 0.00 0.00 0.00 2.44
102 103 0.325602 TACTCCCGCCGTTCCAAAAT 59.674 50.000 0.00 0.00 0.00 1.82
103 104 0.325602 ACTCCCGCCGTTCCAAAATA 59.674 50.000 0.00 0.00 0.00 1.40
104 105 1.014352 CTCCCGCCGTTCCAAAATAG 58.986 55.000 0.00 0.00 0.00 1.73
106 107 1.210967 TCCCGCCGTTCCAAAATAGAT 59.789 47.619 0.00 0.00 0.00 1.98
107 108 1.333619 CCCGCCGTTCCAAAATAGATG 59.666 52.381 0.00 0.00 0.00 2.90
108 109 1.333619 CCGCCGTTCCAAAATAGATGG 59.666 52.381 0.00 0.00 39.41 3.51
109 110 1.268539 CGCCGTTCCAAAATAGATGGC 60.269 52.381 0.00 0.00 37.88 4.40
110 111 1.067060 GCCGTTCCAAAATAGATGGCC 59.933 52.381 0.00 0.00 37.88 5.36
111 112 1.681264 CCGTTCCAAAATAGATGGCCC 59.319 52.381 0.00 0.00 37.88 5.80
112 113 2.374184 CGTTCCAAAATAGATGGCCCA 58.626 47.619 0.00 0.00 37.88 5.36
113 114 2.099098 CGTTCCAAAATAGATGGCCCAC 59.901 50.000 0.00 0.00 37.88 4.61
114 115 2.430694 GTTCCAAAATAGATGGCCCACC 59.569 50.000 0.00 0.00 37.88 4.61
115 116 1.929494 TCCAAAATAGATGGCCCACCT 59.071 47.619 0.00 0.00 37.88 4.00
116 117 2.314549 TCCAAAATAGATGGCCCACCTT 59.685 45.455 0.00 0.00 37.88 3.50
117 118 3.106827 CCAAAATAGATGGCCCACCTTT 58.893 45.455 0.00 0.00 36.63 3.11
119 120 3.473113 AAATAGATGGCCCACCTTTGT 57.527 42.857 0.00 0.00 36.63 2.83
121 122 3.577805 ATAGATGGCCCACCTTTGTAC 57.422 47.619 0.00 0.00 36.63 2.90
122 123 1.372501 AGATGGCCCACCTTTGTACT 58.627 50.000 0.00 0.00 36.63 2.73
123 124 2.557869 AGATGGCCCACCTTTGTACTA 58.442 47.619 0.00 0.00 36.63 1.82
125 126 2.572209 TGGCCCACCTTTGTACTAAC 57.428 50.000 0.00 0.00 36.63 2.34
127 128 2.039348 TGGCCCACCTTTGTACTAACTC 59.961 50.000 0.00 0.00 36.63 3.01
128 129 2.305052 GGCCCACCTTTGTACTAACTCT 59.695 50.000 0.00 0.00 0.00 3.24
129 130 3.597255 GCCCACCTTTGTACTAACTCTC 58.403 50.000 0.00 0.00 0.00 3.20
130 131 3.007614 GCCCACCTTTGTACTAACTCTCA 59.992 47.826 0.00 0.00 0.00 3.27
131 132 4.566987 CCCACCTTTGTACTAACTCTCAC 58.433 47.826 0.00 0.00 0.00 3.51
134 135 5.287226 CACCTTTGTACTAACTCTCACGTT 58.713 41.667 0.00 0.00 0.00 3.99
136 137 5.981915 ACCTTTGTACTAACTCTCACGTTTC 59.018 40.000 0.00 0.00 0.00 2.78
137 138 5.981315 CCTTTGTACTAACTCTCACGTTTCA 59.019 40.000 0.00 0.00 0.00 2.69
138 139 6.477688 CCTTTGTACTAACTCTCACGTTTCAA 59.522 38.462 0.00 0.00 0.00 2.69
139 140 7.010738 CCTTTGTACTAACTCTCACGTTTCAAA 59.989 37.037 0.00 0.00 0.00 2.69
141 142 8.428186 TTGTACTAACTCTCACGTTTCAAAAT 57.572 30.769 0.00 0.00 0.00 1.82
142 143 9.531942 TTGTACTAACTCTCACGTTTCAAAATA 57.468 29.630 0.00 0.00 0.00 1.40
143 144 9.188588 TGTACTAACTCTCACGTTTCAAAATAG 57.811 33.333 0.00 0.00 0.00 1.73
146 147 8.926710 ACTAACTCTCACGTTTCAAAATAGATG 58.073 33.333 0.00 0.00 0.00 2.90
147 148 7.962964 AACTCTCACGTTTCAAAATAGATGA 57.037 32.000 0.00 0.00 0.00 2.92
148 149 7.352719 ACTCTCACGTTTCAAAATAGATGAC 57.647 36.000 0.00 0.00 0.00 3.06
149 150 6.369065 ACTCTCACGTTTCAAAATAGATGACC 59.631 38.462 0.00 0.00 0.00 4.02
151 152 5.309638 TCACGTTTCAAAATAGATGACCCA 58.690 37.500 0.00 0.00 0.00 4.51
157 158 8.434661 CGTTTCAAAATAGATGACCCAATTTTG 58.565 33.333 11.32 11.32 44.73 2.44
161 162 9.308000 TCAAAATAGATGACCCAATTTTGTACT 57.692 29.630 15.19 0.00 44.18 2.73
165 166 9.975218 AATAGATGACCCAATTTTGTACTAAGT 57.025 29.630 0.00 0.00 0.00 2.24
168 169 8.603304 AGATGACCCAATTTTGTACTAAGTAGT 58.397 33.333 0.00 0.00 40.24 2.73
169 170 9.880157 GATGACCCAATTTTGTACTAAGTAGTA 57.120 33.333 0.00 0.00 37.73 1.82
197 198 8.931385 AAATTGGATCATCTATTTTGAAACGG 57.069 30.769 0.00 0.00 0.00 4.44
199 200 6.925610 TGGATCATCTATTTTGAAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
200 201 5.822519 TGGATCATCTATTTTGAAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
201 202 5.239525 GGATCATCTATTTTGAAACGGAGGG 59.760 44.000 0.00 0.00 0.00 4.30
202 203 5.429681 TCATCTATTTTGAAACGGAGGGA 57.570 39.130 0.00 0.00 0.00 4.20
203 204 5.428253 TCATCTATTTTGAAACGGAGGGAG 58.572 41.667 0.00 0.00 0.00 4.30
204 205 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
927 4945 0.464554 GGATAGTGCTGCTTCCCACC 60.465 60.000 0.00 0.00 32.48 4.61
940 4965 2.671070 CCACCACCAGTAGCCCAG 59.329 66.667 0.00 0.00 0.00 4.45
953 4978 2.743928 CCCAGCACGCAGGAAGTC 60.744 66.667 1.43 0.00 0.00 3.01
1186 5238 4.657824 AAGCCGACCACACCGACG 62.658 66.667 0.00 0.00 0.00 5.12
1996 7668 9.194271 GTAAACTCACTCTGTTTTTCTAGGTAG 57.806 37.037 0.00 0.00 38.41 3.18
1997 7669 7.598759 AACTCACTCTGTTTTTCTAGGTAGA 57.401 36.000 0.00 0.00 0.00 2.59
1998 7670 7.784470 ACTCACTCTGTTTTTCTAGGTAGAT 57.216 36.000 0.00 0.00 31.40 1.98
1999 7671 8.880991 ACTCACTCTGTTTTTCTAGGTAGATA 57.119 34.615 0.00 0.00 31.40 1.98
2000 7672 8.741841 ACTCACTCTGTTTTTCTAGGTAGATAC 58.258 37.037 0.00 0.00 31.40 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.585369 TCCATGCCAATATTATTCACTTTCATA 57.415 29.630 0.00 0.00 0.00 2.15
13 14 8.481492 TCCATGCCAATATTATTCACTTTCAT 57.519 30.769 0.00 0.00 0.00 2.57
14 15 7.894753 TCCATGCCAATATTATTCACTTTCA 57.105 32.000 0.00 0.00 0.00 2.69
16 17 8.076910 TGTTCCATGCCAATATTATTCACTTT 57.923 30.769 0.00 0.00 0.00 2.66
17 18 7.658525 TGTTCCATGCCAATATTATTCACTT 57.341 32.000 0.00 0.00 0.00 3.16
19 20 7.326789 CGATTGTTCCATGCCAATATTATTCAC 59.673 37.037 4.18 0.00 31.67 3.18
20 21 7.230309 TCGATTGTTCCATGCCAATATTATTCA 59.770 33.333 4.18 0.00 31.67 2.57
21 22 7.592938 TCGATTGTTCCATGCCAATATTATTC 58.407 34.615 4.18 0.00 31.67 1.75
23 24 7.523293 TTCGATTGTTCCATGCCAATATTAT 57.477 32.000 4.18 0.00 31.67 1.28
24 25 6.951062 TTCGATTGTTCCATGCCAATATTA 57.049 33.333 4.18 0.00 31.67 0.98
26 27 5.850557 TTTCGATTGTTCCATGCCAATAT 57.149 34.783 4.18 0.00 31.67 1.28
27 28 5.651387 TTTTCGATTGTTCCATGCCAATA 57.349 34.783 4.18 0.00 31.67 1.90
28 29 4.533919 TTTTCGATTGTTCCATGCCAAT 57.466 36.364 3.91 3.91 34.11 3.16
29 30 4.533919 ATTTTCGATTGTTCCATGCCAA 57.466 36.364 0.00 0.00 0.00 4.52
30 31 4.533919 AATTTTCGATTGTTCCATGCCA 57.466 36.364 0.00 0.00 0.00 4.92
31 32 5.406649 TGTAATTTTCGATTGTTCCATGCC 58.593 37.500 0.00 0.00 0.00 4.40
32 33 6.321717 TCTGTAATTTTCGATTGTTCCATGC 58.678 36.000 0.00 0.00 0.00 4.06
34 35 8.335356 CGTATCTGTAATTTTCGATTGTTCCAT 58.665 33.333 0.00 0.00 0.00 3.41
35 36 7.546316 TCGTATCTGTAATTTTCGATTGTTCCA 59.454 33.333 0.00 0.00 0.00 3.53
36 37 7.844653 GTCGTATCTGTAATTTTCGATTGTTCC 59.155 37.037 0.00 0.00 0.00 3.62
37 38 7.574481 CGTCGTATCTGTAATTTTCGATTGTTC 59.426 37.037 0.00 0.00 0.00 3.18
38 39 7.388712 CGTCGTATCTGTAATTTTCGATTGTT 58.611 34.615 0.00 0.00 0.00 2.83
39 40 6.020121 CCGTCGTATCTGTAATTTTCGATTGT 60.020 38.462 0.00 0.00 0.00 2.71
41 42 6.267817 TCCGTCGTATCTGTAATTTTCGATT 58.732 36.000 0.00 0.00 0.00 3.34
42 43 5.824429 TCCGTCGTATCTGTAATTTTCGAT 58.176 37.500 0.00 0.00 0.00 3.59
43 44 5.065090 TCTCCGTCGTATCTGTAATTTTCGA 59.935 40.000 0.00 0.00 0.00 3.71
45 46 5.170981 CGTCTCCGTCGTATCTGTAATTTTC 59.829 44.000 0.00 0.00 0.00 2.29
47 48 4.095483 ACGTCTCCGTCGTATCTGTAATTT 59.905 41.667 0.00 0.00 46.28 1.82
50 51 2.621338 ACGTCTCCGTCGTATCTGTAA 58.379 47.619 0.00 0.00 46.28 2.41
51 52 2.299993 ACGTCTCCGTCGTATCTGTA 57.700 50.000 0.00 0.00 46.28 2.74
52 53 2.299993 TACGTCTCCGTCGTATCTGT 57.700 50.000 0.00 0.00 46.28 3.41
57 58 2.286595 GCAATGATACGTCTCCGTCGTA 60.287 50.000 0.00 0.00 46.28 3.43
60 61 1.067212 AGGCAATGATACGTCTCCGTC 59.933 52.381 0.00 0.00 46.28 4.79
62 63 2.225068 AAGGCAATGATACGTCTCCG 57.775 50.000 0.00 0.00 40.83 4.63
63 64 5.116882 AGTAAAAGGCAATGATACGTCTCC 58.883 41.667 0.00 0.00 0.00 3.71
65 66 5.116882 GGAGTAAAAGGCAATGATACGTCT 58.883 41.667 0.00 0.00 0.00 4.18
66 67 4.272748 GGGAGTAAAAGGCAATGATACGTC 59.727 45.833 0.00 0.00 0.00 4.34
67 68 4.196971 GGGAGTAAAAGGCAATGATACGT 58.803 43.478 0.00 0.00 0.00 3.57
68 69 3.247648 CGGGAGTAAAAGGCAATGATACG 59.752 47.826 0.00 0.00 0.00 3.06
69 70 3.003378 GCGGGAGTAAAAGGCAATGATAC 59.997 47.826 0.00 0.00 0.00 2.24
70 71 3.211045 GCGGGAGTAAAAGGCAATGATA 58.789 45.455 0.00 0.00 0.00 2.15
72 73 1.459450 GCGGGAGTAAAAGGCAATGA 58.541 50.000 0.00 0.00 0.00 2.57
74 75 1.029947 CGGCGGGAGTAAAAGGCAAT 61.030 55.000 0.00 0.00 0.00 3.56
75 76 1.673009 CGGCGGGAGTAAAAGGCAA 60.673 57.895 0.00 0.00 0.00 4.52
77 78 1.642037 GAACGGCGGGAGTAAAAGGC 61.642 60.000 13.24 0.00 0.00 4.35
78 79 1.022982 GGAACGGCGGGAGTAAAAGG 61.023 60.000 13.24 0.00 0.00 3.11
79 80 0.320946 TGGAACGGCGGGAGTAAAAG 60.321 55.000 13.24 0.00 0.00 2.27
80 81 0.108207 TTGGAACGGCGGGAGTAAAA 59.892 50.000 13.24 0.00 0.00 1.52
81 82 0.108207 TTTGGAACGGCGGGAGTAAA 59.892 50.000 13.24 3.18 0.00 2.01
82 83 0.108207 TTTTGGAACGGCGGGAGTAA 59.892 50.000 13.24 0.00 0.00 2.24
83 84 0.325602 ATTTTGGAACGGCGGGAGTA 59.674 50.000 13.24 0.00 0.00 2.59
84 85 0.325602 TATTTTGGAACGGCGGGAGT 59.674 50.000 13.24 0.00 0.00 3.85
85 86 1.014352 CTATTTTGGAACGGCGGGAG 58.986 55.000 13.24 0.00 0.00 4.30
87 88 1.333619 CATCTATTTTGGAACGGCGGG 59.666 52.381 13.24 0.00 0.00 6.13
90 91 1.067060 GGCCATCTATTTTGGAACGGC 59.933 52.381 0.00 0.00 36.26 5.68
91 92 1.681264 GGGCCATCTATTTTGGAACGG 59.319 52.381 4.39 0.00 36.26 4.44
92 93 2.099098 GTGGGCCATCTATTTTGGAACG 59.901 50.000 10.70 0.00 36.26 3.95
93 94 2.430694 GGTGGGCCATCTATTTTGGAAC 59.569 50.000 10.70 0.00 36.26 3.62
94 95 2.314549 AGGTGGGCCATCTATTTTGGAA 59.685 45.455 20.14 0.00 36.26 3.53
95 96 1.929494 AGGTGGGCCATCTATTTTGGA 59.071 47.619 20.14 0.00 36.26 3.53
99 100 3.473113 ACAAAGGTGGGCCATCTATTT 57.527 42.857 22.00 9.05 37.19 1.40
100 101 3.527665 AGTACAAAGGTGGGCCATCTATT 59.472 43.478 22.00 13.55 37.19 1.73
101 102 3.123273 AGTACAAAGGTGGGCCATCTAT 58.877 45.455 22.00 11.49 37.19 1.98
102 103 2.557869 AGTACAAAGGTGGGCCATCTA 58.442 47.619 22.00 0.10 37.19 1.98
103 104 1.372501 AGTACAAAGGTGGGCCATCT 58.627 50.000 15.21 15.21 37.19 2.90
104 105 3.014623 GTTAGTACAAAGGTGGGCCATC 58.985 50.000 10.70 10.00 37.19 3.51
106 107 2.039348 GAGTTAGTACAAAGGTGGGCCA 59.961 50.000 0.00 0.00 37.19 5.36
107 108 2.305052 AGAGTTAGTACAAAGGTGGGCC 59.695 50.000 0.00 0.00 0.00 5.80
108 109 3.007614 TGAGAGTTAGTACAAAGGTGGGC 59.992 47.826 0.00 0.00 0.00 5.36
109 110 4.566987 GTGAGAGTTAGTACAAAGGTGGG 58.433 47.826 0.00 0.00 0.00 4.61
110 111 4.235360 CGTGAGAGTTAGTACAAAGGTGG 58.765 47.826 0.00 0.00 0.00 4.61
111 112 4.868067 ACGTGAGAGTTAGTACAAAGGTG 58.132 43.478 0.00 0.00 0.00 4.00
112 113 5.526506 AACGTGAGAGTTAGTACAAAGGT 57.473 39.130 0.00 0.00 31.74 3.50
113 114 5.981315 TGAAACGTGAGAGTTAGTACAAAGG 59.019 40.000 0.00 0.00 33.41 3.11
114 115 7.459394 TTGAAACGTGAGAGTTAGTACAAAG 57.541 36.000 0.00 0.00 33.41 2.77
115 116 7.830940 TTTGAAACGTGAGAGTTAGTACAAA 57.169 32.000 0.00 0.00 33.41 2.83
116 117 7.830940 TTTTGAAACGTGAGAGTTAGTACAA 57.169 32.000 0.00 0.00 33.41 2.41
117 118 9.188588 CTATTTTGAAACGTGAGAGTTAGTACA 57.811 33.333 0.00 0.00 33.41 2.90
121 122 9.140286 TCATCTATTTTGAAACGTGAGAGTTAG 57.860 33.333 0.00 0.00 33.41 2.34
122 123 8.922676 GTCATCTATTTTGAAACGTGAGAGTTA 58.077 33.333 0.00 0.00 33.41 2.24
123 124 7.095187 GGTCATCTATTTTGAAACGTGAGAGTT 60.095 37.037 0.00 0.00 35.59 3.01
125 126 6.183360 GGGTCATCTATTTTGAAACGTGAGAG 60.183 42.308 0.00 0.00 0.00 3.20
127 128 5.411361 TGGGTCATCTATTTTGAAACGTGAG 59.589 40.000 0.00 0.00 0.00 3.51
128 129 5.309638 TGGGTCATCTATTTTGAAACGTGA 58.690 37.500 0.00 0.00 0.00 4.35
129 130 5.621197 TGGGTCATCTATTTTGAAACGTG 57.379 39.130 0.00 0.00 0.00 4.49
130 131 6.834168 ATTGGGTCATCTATTTTGAAACGT 57.166 33.333 0.00 0.00 0.00 3.99
131 132 8.434661 CAAAATTGGGTCATCTATTTTGAAACG 58.565 33.333 14.48 0.00 44.64 3.60
134 135 9.921637 GTACAAAATTGGGTCATCTATTTTGAA 57.078 29.630 21.48 0.00 44.64 2.69
139 140 9.975218 ACTTAGTACAAAATTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
142 143 8.603304 ACTACTTAGTACAAAATTGGGTCATCT 58.397 33.333 0.00 0.00 34.13 2.90
143 144 8.788325 ACTACTTAGTACAAAATTGGGTCATC 57.212 34.615 0.00 0.00 34.13 2.92
172 173 8.748412 TCCGTTTCAAAATAGATGATCCAATTT 58.252 29.630 0.00 0.00 0.00 1.82
173 174 8.292444 TCCGTTTCAAAATAGATGATCCAATT 57.708 30.769 0.00 0.00 0.00 2.32
174 175 7.013655 CCTCCGTTTCAAAATAGATGATCCAAT 59.986 37.037 0.00 0.00 0.00 3.16
175 176 6.318648 CCTCCGTTTCAAAATAGATGATCCAA 59.681 38.462 0.00 0.00 0.00 3.53
176 177 5.822519 CCTCCGTTTCAAAATAGATGATCCA 59.177 40.000 0.00 0.00 0.00 3.41
177 178 5.239525 CCCTCCGTTTCAAAATAGATGATCC 59.760 44.000 0.00 0.00 0.00 3.36
180 181 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
183 184 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
185 186 6.555463 ATCTACTCCCTCCGTTTCAAAATA 57.445 37.500 0.00 0.00 0.00 1.40
186 187 4.903045 TCTACTCCCTCCGTTTCAAAAT 57.097 40.909 0.00 0.00 0.00 1.82
187 188 4.903045 ATCTACTCCCTCCGTTTCAAAA 57.097 40.909 0.00 0.00 0.00 2.44
191 192 4.202131 CCTGTTATCTACTCCCTCCGTTTC 60.202 50.000 0.00 0.00 0.00 2.78
192 193 3.705072 CCTGTTATCTACTCCCTCCGTTT 59.295 47.826 0.00 0.00 0.00 3.60
193 194 3.053095 TCCTGTTATCTACTCCCTCCGTT 60.053 47.826 0.00 0.00 0.00 4.44
194 195 2.512896 TCCTGTTATCTACTCCCTCCGT 59.487 50.000 0.00 0.00 0.00 4.69
196 197 3.232662 GGTCCTGTTATCTACTCCCTCC 58.767 54.545 0.00 0.00 0.00 4.30
197 198 2.885894 CGGTCCTGTTATCTACTCCCTC 59.114 54.545 0.00 0.00 0.00 4.30
199 200 1.962100 CCGGTCCTGTTATCTACTCCC 59.038 57.143 0.00 0.00 0.00 4.30
200 201 1.962100 CCCGGTCCTGTTATCTACTCC 59.038 57.143 0.00 0.00 0.00 3.85
201 202 1.962100 CCCCGGTCCTGTTATCTACTC 59.038 57.143 0.00 0.00 0.00 2.59
202 203 1.572415 TCCCCGGTCCTGTTATCTACT 59.428 52.381 0.00 0.00 0.00 2.57
203 204 2.077687 TCCCCGGTCCTGTTATCTAC 57.922 55.000 0.00 0.00 0.00 2.59
204 205 2.023695 AGTTCCCCGGTCCTGTTATCTA 60.024 50.000 0.00 0.00 0.00 1.98
570 4573 1.009997 TCATGGAGGGAGGGCAAATT 58.990 50.000 0.00 0.00 0.00 1.82
927 4945 2.434884 CGTGCTGGGCTACTGGTG 60.435 66.667 0.00 0.00 0.00 4.17
940 4965 0.380378 TTTGTTGACTTCCTGCGTGC 59.620 50.000 0.00 0.00 0.00 5.34
953 4978 1.851658 CCGGGTGCTTCTTTTTGTTG 58.148 50.000 0.00 0.00 0.00 3.33
1996 7668 5.460419 CCAAGATAGAGCGAGTTGTTGTATC 59.540 44.000 3.85 3.85 35.21 2.24
1997 7669 5.127194 TCCAAGATAGAGCGAGTTGTTGTAT 59.873 40.000 0.00 0.00 0.00 2.29
1998 7670 4.461431 TCCAAGATAGAGCGAGTTGTTGTA 59.539 41.667 0.00 0.00 0.00 2.41
1999 7671 3.258372 TCCAAGATAGAGCGAGTTGTTGT 59.742 43.478 0.00 0.00 0.00 3.32
2000 7672 3.849911 TCCAAGATAGAGCGAGTTGTTG 58.150 45.455 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.