Multiple sequence alignment - TraesCS2D01G330700

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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 TraesCS2D01G330700 chr2D 100.000 2312 0 0 1 2312 423348631 423346320 0.000000e+00 4270.0
1 TraesCS2D01G330700 chr2D 85.044 682 54 25 792 1449 423292546 423291889 0.000000e+00 651.0
2 TraesCS2D01G330700 chr2D 89.879 247 13 4 504 746 423292782 423292544 8.020000e-80 307.0
3 TraesCS2D01G330700 chr2D 91.710 193 12 2 106 294 540163582 540163774 4.900000e-67 265.0
4 TraesCS2D01G330700 chr2D 91.803 183 12 2 2131 2312 559233658 559233478 3.810000e-63 252.0
5 TraesCS2D01G330700 chr2A 92.028 991 43 10 504 1480 565234025 565234993 0.000000e+00 1360.0
6 TraesCS2D01G330700 chr2A 85.141 922 90 20 579 1480 565282678 565283572 0.000000e+00 900.0
7 TraesCS2D01G330700 chr2A 86.738 558 38 15 772 1325 565262352 565262877 2.560000e-164 588.0
8 TraesCS2D01G330700 chr2A 84.275 655 48 21 874 1480 565313453 565314100 2.560000e-164 588.0
9 TraesCS2D01G330700 chr2A 85.232 237 10 4 291 502 565233742 565233978 1.080000e-53 220.0
10 TraesCS2D01G330700 chr2A 95.536 112 5 0 1 112 565233639 565233750 1.830000e-41 180.0
11 TraesCS2D01G330700 chr2A 81.526 249 15 14 507 754 565270001 565270219 2.360000e-40 176.0
12 TraesCS2D01G330700 chr2A 85.496 131 19 0 1491 1621 565263492 565263622 1.110000e-28 137.0
13 TraesCS2D01G330700 chr2A 89.899 99 10 0 291 389 565280519 565280617 6.700000e-26 128.0
14 TraesCS2D01G330700 chr2A 88.119 101 12 0 291 391 565267423 565267523 1.120000e-23 121.0
15 TraesCS2D01G330700 chr2A 90.805 87 8 0 1492 1578 565258840 565258926 1.450000e-22 117.0
16 TraesCS2D01G330700 chr2A 100.000 32 0 0 291 322 565243297 565243328 2.480000e-05 60.2
17 TraesCS2D01G330700 chr2B 94.509 692 32 2 780 1465 496542430 496541739 0.000000e+00 1062.0
18 TraesCS2D01G330700 chr2B 86.968 729 53 20 587 1301 496351408 496350708 0.000000e+00 782.0
19 TraesCS2D01G330700 chr2B 87.047 718 54 19 587 1290 496355722 496355030 0.000000e+00 774.0
20 TraesCS2D01G330700 chr2B 86.908 718 55 19 587 1290 496353565 496352873 0.000000e+00 769.0
21 TraesCS2D01G330700 chr2B 82.385 914 78 43 606 1475 496078987 496078113 0.000000e+00 719.0
22 TraesCS2D01G330700 chr2B 82.010 806 90 29 601 1383 496360042 496359269 3.240000e-178 634.0
23 TraesCS2D01G330700 chr2B 85.208 649 58 19 720 1350 496177294 496176666 1.170000e-177 632.0
24 TraesCS2D01G330700 chr2B 84.804 612 50 19 703 1301 496088019 496087438 1.990000e-160 575.0
25 TraesCS2D01G330700 chr2B 85.127 511 42 12 796 1298 496118340 496117856 2.060000e-135 492.0
26 TraesCS2D01G330700 chr2B 89.443 341 22 7 1513 1851 496540295 496539967 3.550000e-113 418.0
27 TraesCS2D01G330700 chr2B 94.681 188 6 2 509 696 496542655 496542472 2.910000e-74 289.0
28 TraesCS2D01G330700 chr2B 79.625 427 42 16 1688 2084 504323623 504323212 4.900000e-67 265.0
29 TraesCS2D01G330700 chr2B 90.148 203 15 3 1457 1654 496175971 496175769 2.280000e-65 259.0
30 TraesCS2D01G330700 chr2B 91.848 184 10 4 2131 2312 365952856 365952676 3.810000e-63 252.0
31 TraesCS2D01G330700 chr2B 85.833 240 8 7 291 505 496542940 496542702 4.970000e-57 231.0
32 TraesCS2D01G330700 chr2B 86.857 175 16 5 1479 1649 496117639 496117468 3.030000e-44 189.0
33 TraesCS2D01G330700 chr2B 96.429 112 4 0 1 112 496543043 496542932 3.920000e-43 185.0
34 TraesCS2D01G330700 chr2B 93.204 103 6 1 1347 1449 496176299 496176198 1.430000e-32 150.0
35 TraesCS2D01G330700 chr2B 92.593 81 6 0 291 371 496143175 496143095 1.450000e-22 117.0
36 TraesCS2D01G330700 chr2B 100.000 29 0 0 427 455 496512940 496512912 1.000000e-03 54.7
37 TraesCS2D01G330700 chr3B 81.236 453 44 12 1688 2113 673282283 673281845 6.160000e-86 327.0
38 TraesCS2D01G330700 chr3B 80.263 456 45 7 1688 2113 7141219 7141659 3.730000e-78 302.0
39 TraesCS2D01G330700 chr3B 80.310 452 42 10 1693 2113 436517655 436518090 4.830000e-77 298.0
40 TraesCS2D01G330700 chr3B 78.540 452 52 19 1688 2108 807730186 807730623 2.950000e-64 255.0
41 TraesCS2D01G330700 chr3B 91.803 183 12 2 2131 2312 50156200 50156380 3.810000e-63 252.0
42 TraesCS2D01G330700 chr3B 91.803 183 12 2 2131 2312 436518379 436518559 3.810000e-63 252.0
43 TraesCS2D01G330700 chr4B 80.973 452 41 10 1688 2108 635026746 635026309 1.330000e-82 316.0
44 TraesCS2D01G330700 chr4B 89.730 185 15 4 113 295 163868547 163868365 1.380000e-57 233.0
45 TraesCS2D01G330700 chr5B 80.263 456 45 13 1688 2113 57966463 57966903 3.730000e-78 302.0
46 TraesCS2D01G330700 chr5B 91.803 183 12 2 2131 2312 278651726 278651546 3.810000e-63 252.0
47 TraesCS2D01G330700 chr5B 91.803 183 12 2 2131 2312 381351432 381351252 3.810000e-63 252.0
48 TraesCS2D01G330700 chr1B 79.476 458 45 11 1688 2113 38114149 38114589 1.750000e-71 279.0
49 TraesCS2D01G330700 chr1D 79.167 456 50 15 1688 2113 21877960 21878400 8.140000e-70 274.0
50 TraesCS2D01G330700 chr1D 91.803 183 12 2 2131 2312 464917510 464917690 3.810000e-63 252.0
51 TraesCS2D01G330700 chrUn 78.947 456 51 12 1688 2113 293416 292976 3.790000e-68 268.0
52 TraesCS2D01G330700 chrUn 91.758 182 13 1 2131 2312 292674 292495 3.810000e-63 252.0
53 TraesCS2D01G330700 chr3D 92.432 185 11 3 113 295 533955515 533955698 6.340000e-66 261.0
54 TraesCS2D01G330700 chr3D 90.625 192 15 2 112 301 167560932 167560742 3.810000e-63 252.0
55 TraesCS2D01G330700 chr7B 92.308 182 13 1 113 294 196133959 196133779 8.200000e-65 257.0
56 TraesCS2D01G330700 chr7B 91.803 183 12 2 2131 2312 69543379 69543559 3.810000e-63 252.0
57 TraesCS2D01G330700 chr5D 92.308 182 13 1 113 294 96030978 96031158 8.200000e-65 257.0
58 TraesCS2D01G330700 chr5A 92.737 179 11 2 111 287 101083272 101083450 8.200000e-65 257.0
59 TraesCS2D01G330700 chr7D 90.404 198 12 5 105 295 625764002 625763805 1.060000e-63 254.0
60 TraesCS2D01G330700 chr7D 89.848 197 17 1 105 298 31996734 31996930 1.370000e-62 250.0


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 TraesCS2D01G330700 chr2D 423346320 423348631 2311 True 4270.000000 4270 100.00000 1 2312 1 chr2D.!!$R1 2311
1 TraesCS2D01G330700 chr2D 423291889 423292782 893 True 479.000000 651 87.46150 504 1449 2 chr2D.!!$R3 945
2 TraesCS2D01G330700 chr2A 565313453 565314100 647 False 588.000000 588 84.27500 874 1480 1 chr2A.!!$F2 606
3 TraesCS2D01G330700 chr2A 565233639 565234993 1354 False 586.666667 1360 90.93200 1 1480 3 chr2A.!!$F3 1479
4 TraesCS2D01G330700 chr2A 565280519 565283572 3053 False 514.000000 900 87.52000 291 1480 2 chr2A.!!$F5 1189
5 TraesCS2D01G330700 chr2A 565258840 565270219 11379 False 227.800000 588 86.53680 291 1621 5 chr2A.!!$F4 1330
6 TraesCS2D01G330700 chr2B 496350708 496360042 9334 True 739.750000 782 85.73325 587 1383 4 chr2B.!!$R9 796
7 TraesCS2D01G330700 chr2B 496078113 496078987 874 True 719.000000 719 82.38500 606 1475 1 chr2B.!!$R2 869
8 TraesCS2D01G330700 chr2B 496087438 496088019 581 True 575.000000 575 84.80400 703 1301 1 chr2B.!!$R3 598
9 TraesCS2D01G330700 chr2B 496539967 496543043 3076 True 437.000000 1062 92.17900 1 1851 5 chr2B.!!$R10 1850
10 TraesCS2D01G330700 chr2B 496175769 496177294 1525 True 347.000000 632 89.52000 720 1654 3 chr2B.!!$R8 934
11 TraesCS2D01G330700 chr2B 496117468 496118340 872 True 340.500000 492 85.99200 796 1649 2 chr2B.!!$R7 853
12 TraesCS2D01G330700 chr3B 436517655 436518559 904 False 275.000000 298 86.05650 1693 2312 2 chr3B.!!$F4 619
13 TraesCS2D01G330700 chrUn 292495 293416 921 True 260.000000 268 85.35250 1688 2312 2 chrUn.!!$R1 624

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
773 5473 0.034896 AACACGAGCATTTCCGGAGT 59.965 50.0 3.34 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 17006 1.12478 GGCTAGGGTTTCCTCCTCTC 58.875 60.0 0.0 0.0 43.66 3.2 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
103 104 4.939052 TCCACTTTTATTTTTGCGGGAA 57.061 36.364 0.00 0.00 0.00 3.97
104 105 5.476091 TCCACTTTTATTTTTGCGGGAAT 57.524 34.783 0.00 0.00 0.00 3.01
105 106 5.859495 TCCACTTTTATTTTTGCGGGAATT 58.141 33.333 0.00 0.00 0.00 2.17
106 107 6.994221 TCCACTTTTATTTTTGCGGGAATTA 58.006 32.000 0.00 0.00 0.00 1.40
108 109 6.871492 CCACTTTTATTTTTGCGGGAATTAGT 59.129 34.615 0.00 0.00 0.00 2.24
118 119 5.365403 TGCGGGAATTAGTTTACAGTTTG 57.635 39.130 0.00 0.00 0.00 2.93
121 122 5.180680 GCGGGAATTAGTTTACAGTTTGTCT 59.819 40.000 0.00 0.00 0.00 3.41
137 138 9.376075 ACAGTTTGTCTAATTCACATCTAGATG 57.624 33.333 27.63 27.63 44.15 2.90
165 166 8.561738 TTTTAAGGATGTCACATCTAAACTCC 57.438 34.615 17.46 0.18 0.00 3.85
168 169 4.080863 AGGATGTCACATCTAAACTCCCAC 60.081 45.833 17.46 0.00 0.00 4.61
169 170 4.323485 GGATGTCACATCTAAACTCCCACA 60.323 45.833 17.46 0.00 0.00 4.17
170 171 4.698201 TGTCACATCTAAACTCCCACAA 57.302 40.909 0.00 0.00 0.00 3.33
171 172 5.042463 TGTCACATCTAAACTCCCACAAA 57.958 39.130 0.00 0.00 0.00 2.83
173 174 6.774673 TGTCACATCTAAACTCCCACAAATA 58.225 36.000 0.00 0.00 0.00 1.40
184 185 7.524717 AACTCCCACAAATATATAATGCACC 57.475 36.000 0.00 0.00 0.00 5.01
188 189 9.241919 CTCCCACAAATATATAATGCACCAATA 57.758 33.333 0.00 0.00 0.00 1.90
240 241 4.214980 CACAAACAGAGTGGACATCAAC 57.785 45.455 0.00 0.00 33.43 3.18
241 242 3.879295 CACAAACAGAGTGGACATCAACT 59.121 43.478 0.00 0.00 33.43 3.16
243 244 5.527214 CACAAACAGAGTGGACATCAACTTA 59.473 40.000 0.00 0.00 33.43 2.24
245 246 5.808366 AACAGAGTGGACATCAACTTAGA 57.192 39.130 0.00 0.00 0.00 2.10
246 247 6.365970 AACAGAGTGGACATCAACTTAGAT 57.634 37.500 0.00 0.00 0.00 1.98
319 1667 7.824779 AGTTTAACCTGATTCATTAGGTCAGAC 59.175 37.037 3.83 0.00 44.98 3.51
502 5120 2.961526 ATGATGAGGACGCGTTTACT 57.038 45.000 15.53 12.81 0.00 2.24
764 5464 4.063967 TCGCCCGAACACGAGCAT 62.064 61.111 0.00 0.00 33.69 3.79
765 5465 3.118454 CGCCCGAACACGAGCATT 61.118 61.111 0.00 0.00 30.58 3.56
766 5466 2.677003 CGCCCGAACACGAGCATTT 61.677 57.895 0.00 0.00 30.58 2.32
767 5467 1.134694 GCCCGAACACGAGCATTTC 59.865 57.895 0.00 0.00 31.47 2.17
768 5468 1.794222 CCCGAACACGAGCATTTCC 59.206 57.895 0.00 0.00 0.00 3.13
769 5469 1.419922 CCGAACACGAGCATTTCCG 59.580 57.895 0.00 0.00 0.00 4.30
770 5470 1.419922 CGAACACGAGCATTTCCGG 59.580 57.895 0.00 0.00 0.00 5.14
771 5471 1.011968 CGAACACGAGCATTTCCGGA 61.012 55.000 0.00 0.00 0.00 5.14
772 5472 0.721718 GAACACGAGCATTTCCGGAG 59.278 55.000 3.34 0.00 0.00 4.63
773 5473 0.034896 AACACGAGCATTTCCGGAGT 59.965 50.000 3.34 0.00 0.00 3.85
774 5474 0.034896 ACACGAGCATTTCCGGAGTT 59.965 50.000 3.34 0.00 0.00 3.01
775 5475 1.156736 CACGAGCATTTCCGGAGTTT 58.843 50.000 3.34 0.00 0.00 2.66
776 5476 1.128692 CACGAGCATTTCCGGAGTTTC 59.871 52.381 3.34 0.00 0.00 2.78
777 5477 1.002087 ACGAGCATTTCCGGAGTTTCT 59.998 47.619 3.34 0.71 0.00 2.52
778 5478 1.394917 CGAGCATTTCCGGAGTTTCTG 59.605 52.381 3.34 0.29 0.00 3.02
816 5539 1.614317 GGCATCTAACAACCCAGCAGT 60.614 52.381 0.00 0.00 0.00 4.40
1302 10388 1.985662 CCACCACCAGTACCCGCTA 60.986 63.158 0.00 0.00 0.00 4.26
1325 10449 2.290323 ACTTCTGACCATGTAACTGCCC 60.290 50.000 0.00 0.00 0.00 5.36
1449 10973 7.959689 ACTCTATCTATTTACGAGTTCGCTA 57.040 36.000 0.73 0.00 44.43 4.26
1465 11208 3.793559 TCGCTAGGCTAATTTCCAGTTC 58.206 45.455 0.00 0.00 0.00 3.01
1493 11366 8.668510 AATCAAGAAAACAGCACGATAGATAT 57.331 30.769 0.00 0.00 41.38 1.63
1586 12827 2.897326 TCGTCCAATCATATGATCGGGT 59.103 45.455 20.32 2.56 29.66 5.28
1587 12829 4.082408 GTCGTCCAATCATATGATCGGGTA 60.082 45.833 20.32 11.51 29.66 3.69
1633 12875 3.329929 AACCACGATCCTGTAAGAACC 57.670 47.619 0.00 0.00 34.07 3.62
1682 12924 2.433868 TCAAGTCTGTACCAACGAGC 57.566 50.000 0.00 0.00 0.00 5.03
1708 17002 2.997315 CTCTGGTGCTCCCACGGA 60.997 66.667 1.59 0.00 43.00 4.69
1848 17154 1.574428 GCGCTTTTTCCTTCTCGCA 59.426 52.632 0.00 0.00 41.84 5.10
1866 17188 4.523512 GGGCGATCTACCCTAGCT 57.476 61.111 12.35 0.00 44.68 3.32
1872 17194 2.100916 GCGATCTACCCTAGCTGAAACA 59.899 50.000 0.00 0.00 0.00 2.83
1945 17281 3.807538 CTGCGTGCTGGTGATGGC 61.808 66.667 0.00 0.00 0.00 4.40
1949 17285 1.079197 CGTGCTGGTGATGGCTACA 60.079 57.895 0.00 0.00 0.00 2.74
1953 17289 2.125147 TGGTGATGGCTACAGCGC 60.125 61.111 0.00 0.00 42.47 5.92
1980 17316 3.181422 TGGTCGACCTACCAGATATGGAT 60.181 47.826 33.39 0.00 44.68 3.41
1982 17318 3.193691 GTCGACCTACCAGATATGGATGG 59.806 52.174 14.70 15.95 42.60 3.51
1983 17319 3.075432 TCGACCTACCAGATATGGATGGA 59.925 47.826 22.36 7.16 39.02 3.41
1985 17321 4.421131 GACCTACCAGATATGGATGGAGT 58.579 47.826 22.36 9.70 39.02 3.85
2084 17445 1.963338 GTCTTGCTGGTTGCTCGCT 60.963 57.895 0.00 0.00 43.37 4.93
2098 17459 1.272781 CTCGCTGGATTCGTCTTGTC 58.727 55.000 0.00 0.00 0.00 3.18
2108 17469 2.939022 GTCTTGTCGCTTGCGCTT 59.061 55.556 9.73 0.00 0.00 4.68
2121 17482 2.978010 CGCTTGGCCCACTCGTTT 60.978 61.111 0.00 0.00 0.00 3.60
2125 17486 1.076632 TTGGCCCACTCGTTTGGTT 60.077 52.632 0.00 0.00 34.44 3.67
2126 17487 1.388065 TTGGCCCACTCGTTTGGTTG 61.388 55.000 0.00 0.00 34.44 3.77
2128 17489 2.485795 GCCCACTCGTTTGGTTGCA 61.486 57.895 4.67 0.00 34.44 4.08
2129 17490 1.805428 GCCCACTCGTTTGGTTGCAT 61.805 55.000 0.00 0.00 34.44 3.96
2172 19420 0.250640 ACTACTGTCGACCCACTCGT 60.251 55.000 14.12 3.33 43.45 4.18
2181 19429 1.498865 GACCCACTCGTGTGCTGTTG 61.499 60.000 12.06 0.00 42.54 3.33
2265 19514 3.009363 TCTCTTGGGAGCATCATTTGTGA 59.991 43.478 0.00 0.00 39.31 3.58
2298 19547 1.152030 ACAGAGGCAGGAGGTGGAA 60.152 57.895 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.916440 TCTGGATGCATGCATTGATAAATAC 58.084 36.000 32.60 16.72 36.70 1.89
106 107 9.561069 AGATGTGAATTAGACAAACTGTAAACT 57.439 29.630 0.00 0.00 0.00 2.66
139 140 9.010029 GGAGTTTAGATGTGACATCCTTAAAAA 57.990 33.333 21.05 11.39 0.00 1.94
140 141 7.610305 GGGAGTTTAGATGTGACATCCTTAAAA 59.390 37.037 21.05 13.52 0.00 1.52
146 147 4.192317 GTGGGAGTTTAGATGTGACATCC 58.808 47.826 21.05 6.28 0.00 3.51
148 149 4.908601 TGTGGGAGTTTAGATGTGACAT 57.091 40.909 0.00 0.00 0.00 3.06
160 161 7.066142 TGGTGCATTATATATTTGTGGGAGTT 58.934 34.615 0.00 0.00 0.00 3.01
162 163 7.523293 TTGGTGCATTATATATTTGTGGGAG 57.477 36.000 0.00 0.00 0.00 4.30
220 221 4.156455 AGTTGATGTCCACTCTGTTTGT 57.844 40.909 0.00 0.00 0.00 2.83
222 223 6.174720 TCTAAGTTGATGTCCACTCTGTTT 57.825 37.500 0.00 0.00 0.00 2.83
224 225 5.728471 CATCTAAGTTGATGTCCACTCTGT 58.272 41.667 6.97 0.00 39.05 3.41
263 264 9.019656 GGATCTGTCTAGAACACATCTATATGT 57.980 37.037 0.00 0.00 40.74 2.29
264 265 9.018582 TGGATCTGTCTAGAACACATCTATATG 57.981 37.037 0.00 0.00 39.88 1.78
265 266 9.766754 ATGGATCTGTCTAGAACACATCTATAT 57.233 33.333 0.00 0.00 39.88 0.86
266 267 9.593565 AATGGATCTGTCTAGAACACATCTATA 57.406 33.333 0.00 0.00 39.88 1.31
267 268 8.489676 AATGGATCTGTCTAGAACACATCTAT 57.510 34.615 0.00 0.00 39.88 1.98
268 269 7.904558 AATGGATCTGTCTAGAACACATCTA 57.095 36.000 0.00 0.00 39.71 1.98
270 271 7.721402 ACTAATGGATCTGTCTAGAACACATC 58.279 38.462 0.00 0.00 36.32 3.06
271 272 7.667575 ACTAATGGATCTGTCTAGAACACAT 57.332 36.000 0.00 0.00 36.32 3.21
273 274 9.871238 TTAAACTAATGGATCTGTCTAGAACAC 57.129 33.333 0.00 0.00 36.32 3.32
275 276 9.315525 GGTTAAACTAATGGATCTGTCTAGAAC 57.684 37.037 0.00 0.00 36.32 3.01
278 279 8.696374 TCAGGTTAAACTAATGGATCTGTCTAG 58.304 37.037 0.00 0.00 0.00 2.43
283 284 8.737168 TGAATCAGGTTAAACTAATGGATCTG 57.263 34.615 0.00 0.00 0.00 2.90
287 288 9.627123 CCTAATGAATCAGGTTAAACTAATGGA 57.373 33.333 0.00 0.00 0.00 3.41
319 1667 3.058520 CGTTCACAGGTTATACGTCAACG 59.941 47.826 0.00 0.12 46.33 4.10
663 5337 6.543831 GTGATGATTTTGTGAAGGGTATAGCT 59.456 38.462 1.32 0.00 0.00 3.32
664 5338 6.318648 TGTGATGATTTTGTGAAGGGTATAGC 59.681 38.462 0.00 0.00 0.00 2.97
665 5339 7.012704 CCTGTGATGATTTTGTGAAGGGTATAG 59.987 40.741 0.00 0.00 0.00 1.31
666 5340 6.828273 CCTGTGATGATTTTGTGAAGGGTATA 59.172 38.462 0.00 0.00 0.00 1.47
764 5464 2.833631 GGAGACAGAAACTCCGGAAA 57.166 50.000 5.23 0.00 43.25 3.13
770 5470 1.611936 GCCAAGGGGAGACAGAAACTC 60.612 57.143 0.00 0.00 35.59 3.01
771 5471 0.402121 GCCAAGGGGAGACAGAAACT 59.598 55.000 0.00 0.00 35.59 2.66
772 5472 0.110486 TGCCAAGGGGAGACAGAAAC 59.890 55.000 0.00 0.00 35.59 2.78
773 5473 0.401738 CTGCCAAGGGGAGACAGAAA 59.598 55.000 0.00 0.00 44.17 2.52
774 5474 2.069776 CTGCCAAGGGGAGACAGAA 58.930 57.895 0.00 0.00 44.17 3.02
775 5475 2.596851 GCTGCCAAGGGGAGACAGA 61.597 63.158 8.06 0.00 44.17 3.41
776 5476 1.267574 TAGCTGCCAAGGGGAGACAG 61.268 60.000 8.06 0.00 44.17 3.51
777 5477 1.229496 TAGCTGCCAAGGGGAGACA 60.229 57.895 8.06 0.00 44.17 3.41
778 5478 1.524482 CTAGCTGCCAAGGGGAGAC 59.476 63.158 8.06 0.00 44.17 3.36
816 5539 2.026262 GGGTTCCTCACCTTCATTGCTA 60.026 50.000 0.00 0.00 46.38 3.49
859 5586 5.622770 ACACGAGAAGTCAACAAAAACTT 57.377 34.783 0.00 0.00 38.40 2.66
1077 5831 4.631740 TGGTCCCTGGCGTCTCCA 62.632 66.667 0.00 0.00 44.18 3.86
1302 10388 4.384208 GGGCAGTTACATGGTCAGAAGTAT 60.384 45.833 0.00 0.00 0.00 2.12
1325 10449 4.416620 AGAGTACTTCAAAATCGCTCTCG 58.583 43.478 0.00 0.00 0.00 4.04
1358 10867 7.270047 ACACGCCTATGTATATTTGTAGTTGT 58.730 34.615 0.00 0.00 0.00 3.32
1377 10890 7.254852 TCCTTCAATGAATTAATAAACACGCC 58.745 34.615 0.00 0.00 0.00 5.68
1417 10933 9.059260 ACTCGTAAATAGATAGAGTTTCTCTCC 57.941 37.037 2.41 0.00 43.71 3.71
1449 10973 5.253330 TGATTTCGAACTGGAAATTAGCCT 58.747 37.500 0.00 0.00 44.41 4.58
1465 11208 3.872354 TCGTGCTGTTTTCTTGATTTCG 58.128 40.909 0.00 0.00 0.00 3.46
1493 11366 6.408092 CCTTTTCCTGCAGGTGACATACTATA 60.408 42.308 31.58 5.39 36.34 1.31
1500 11373 0.550914 ACCTTTTCCTGCAGGTGACA 59.449 50.000 31.58 10.48 42.20 3.58
1511 12752 2.410939 GTGTGACGTCCTACCTTTTCC 58.589 52.381 14.12 0.00 0.00 3.13
1633 12875 6.893958 ATTTAGTAGTGCAGATCTTGTTCG 57.106 37.500 0.00 0.00 0.00 3.95
1708 17002 1.612739 GGGTTTCCTCCTCTCCCGT 60.613 63.158 0.00 0.00 0.00 5.28
1712 17006 1.124780 GGCTAGGGTTTCCTCCTCTC 58.875 60.000 0.00 0.00 43.66 3.20
1715 17009 2.368011 GCGGCTAGGGTTTCCTCCT 61.368 63.158 0.00 0.00 43.66 3.69
1863 17185 2.972505 CCACGCCGTGTTTCAGCT 60.973 61.111 16.99 0.00 0.00 4.24
1866 17188 3.578272 GCACCACGCCGTGTTTCA 61.578 61.111 16.99 0.00 36.08 2.69
1945 17281 4.814294 GACCACCGGGCGCTGTAG 62.814 72.222 7.64 0.00 37.90 2.74
1965 17301 3.517100 CCACTCCATCCATATCTGGTAGG 59.483 52.174 0.00 1.25 43.61 3.18
1968 17304 2.342659 CCCACTCCATCCATATCTGGT 58.657 52.381 0.00 0.00 43.61 4.00
1971 17307 2.050754 CCCCCACTCCATCCATATCT 57.949 55.000 0.00 0.00 0.00 1.98
2020 17356 3.607661 GGGATCTCGCCCGACTCC 61.608 72.222 0.00 6.16 38.58 3.85
2084 17445 1.428448 CAAGCGACAAGACGAATCCA 58.572 50.000 0.00 0.00 35.09 3.41
2108 17469 1.826054 CAACCAAACGAGTGGGCCA 60.826 57.895 0.00 0.00 43.56 5.36
2114 17475 2.571212 TCAAGATGCAACCAAACGAGT 58.429 42.857 0.00 0.00 0.00 4.18
2119 17480 3.306225 GCCTTCATCAAGATGCAACCAAA 60.306 43.478 5.19 0.00 38.65 3.28
2121 17482 1.820519 GCCTTCATCAAGATGCAACCA 59.179 47.619 5.19 0.00 38.65 3.67
2172 19420 3.723097 TTTCCCCCGCAACAGCACA 62.723 57.895 0.00 0.00 0.00 4.57
2214 19463 3.695606 ACAGTGCCGCCATCGTCT 61.696 61.111 0.00 0.00 0.00 4.18
2265 19514 1.670406 CTGTCTTCCTGCGCTGCTT 60.670 57.895 9.73 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.