Multiple sequence alignment - TraesCS1A01G393600

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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 TraesCS1A01G393600 chr1A 100.000 2393 0 0 1 2393 559980283 559977891 0.000000e+00 4420.0
1 TraesCS1A01G393600 chr1A 86.201 1174 100 38 888 2040 559886983 559885851 0.000000e+00 1214.0
2 TraesCS1A01G393600 chr1A 88.488 1025 57 28 676 1640 559942197 559941174 0.000000e+00 1182.0
3 TraesCS1A01G393600 chr1A 94.226 433 24 1 1711 2142 559941177 559940745 0.000000e+00 660.0
4 TraesCS1A01G393600 chr1A 83.308 647 66 20 65 679 559929953 559929317 2.080000e-155 558.0
5 TraesCS1A01G393600 chr1A 80.775 723 83 25 1 678 559943262 559942551 4.560000e-142 514.0
6 TraesCS1A01G393600 chr1A 94.779 249 12 1 2136 2383 559934922 559934674 1.040000e-103 387.0
7 TraesCS1A01G393600 chr1A 86.087 115 9 3 2052 2166 559885771 559885664 1.500000e-22 117.0
8 TraesCS1A01G393600 chr5D 85.026 1349 92 60 675 1964 462746068 462747365 0.000000e+00 1271.0
9 TraesCS1A01G393600 chr5D 85.239 752 52 27 1346 2051 462670009 462670747 0.000000e+00 719.0
10 TraesCS1A01G393600 chr5D 87.065 603 42 18 675 1243 462669404 462670004 0.000000e+00 649.0
11 TraesCS1A01G393600 chr5D 82.300 661 78 20 744 1381 462895413 462896057 9.740000e-149 536.0
12 TraesCS1A01G393600 chr5D 88.811 286 23 6 2106 2383 462897628 462897912 2.280000e-90 342.0
13 TraesCS1A01G393600 chr5D 84.071 226 25 2 2106 2322 462752621 462752844 8.670000e-50 207.0
14 TraesCS1A01G393600 chrUn 84.576 1381 97 61 743 2051 67088228 67086892 0.000000e+00 1264.0
15 TraesCS1A01G393600 chrUn 84.576 1381 97 61 743 2051 307431406 307432742 0.000000e+00 1264.0
16 TraesCS1A01G393600 chrUn 85.451 543 64 11 819 1351 199466141 199465604 3.480000e-153 551.0
17 TraesCS1A01G393600 chr5A 86.474 865 54 32 675 1507 582652639 582653472 0.000000e+00 891.0
18 TraesCS1A01G393600 chr5A 82.802 721 88 24 691 1381 582886919 582887633 1.570000e-171 612.0
19 TraesCS1A01G393600 chr5A 85.185 540 44 15 1528 2035 582654464 582654999 2.730000e-144 521.0
20 TraesCS1A01G393600 chr5A 86.667 285 31 5 2106 2383 582890085 582890369 2.310000e-80 309.0
21 TraesCS1A01G393600 chr5A 80.534 262 35 10 1799 2051 582889689 582889943 1.130000e-43 187.0
22 TraesCS1A01G393600 chr5B 86.374 844 60 22 1214 2023 569148462 569149284 0.000000e+00 870.0
23 TraesCS1A01G393600 chr5B 86.019 844 63 22 1214 2023 569249676 569250498 0.000000e+00 854.0
24 TraesCS1A01G393600 chr5B 82.511 709 83 21 678 1351 569224138 569224840 3.430000e-163 584.0
25 TraesCS1A01G393600 chr5B 90.566 106 8 2 676 781 569140549 569140652 3.210000e-29 139.0
26 TraesCS1A01G393600 chr5B 90.566 106 8 2 676 781 569241725 569241828 3.210000e-29 139.0
27 TraesCS1A01G393600 chr5B 100.000 49 0 0 819 867 569241841 569241889 9.110000e-15 91.6
28 TraesCS1A01G393600 chr5B 97.959 49 1 0 819 867 569140665 569140713 4.240000e-13 86.1


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 TraesCS1A01G393600 chr1A 559977891 559980283 2392 True 4420.000000 4420 100.000000 1 2393 1 chr1A.!!$R3 2392
1 TraesCS1A01G393600 chr1A 559940745 559943262 2517 True 785.333333 1182 87.829667 1 2142 3 chr1A.!!$R5 2141
2 TraesCS1A01G393600 chr1A 559885664 559886983 1319 True 665.500000 1214 86.144000 888 2166 2 chr1A.!!$R4 1278
3 TraesCS1A01G393600 chr1A 559929317 559929953 636 True 558.000000 558 83.308000 65 679 1 chr1A.!!$R1 614
4 TraesCS1A01G393600 chr5D 462746068 462747365 1297 False 1271.000000 1271 85.026000 675 1964 1 chr5D.!!$F1 1289
5 TraesCS1A01G393600 chr5D 462669404 462670747 1343 False 684.000000 719 86.152000 675 2051 2 chr5D.!!$F3 1376
6 TraesCS1A01G393600 chr5D 462895413 462897912 2499 False 439.000000 536 85.555500 744 2383 2 chr5D.!!$F4 1639
7 TraesCS1A01G393600 chrUn 67086892 67088228 1336 True 1264.000000 1264 84.576000 743 2051 1 chrUn.!!$R1 1308
8 TraesCS1A01G393600 chrUn 307431406 307432742 1336 False 1264.000000 1264 84.576000 743 2051 1 chrUn.!!$F1 1308
9 TraesCS1A01G393600 chrUn 199465604 199466141 537 True 551.000000 551 85.451000 819 1351 1 chrUn.!!$R2 532
10 TraesCS1A01G393600 chr5A 582652639 582654999 2360 False 706.000000 891 85.829500 675 2035 2 chr5A.!!$F1 1360
11 TraesCS1A01G393600 chr5A 582886919 582890369 3450 False 369.333333 612 83.334333 691 2383 3 chr5A.!!$F2 1692
12 TraesCS1A01G393600 chr5B 569148462 569149284 822 False 870.000000 870 86.374000 1214 2023 1 chr5B.!!$F1 809
13 TraesCS1A01G393600 chr5B 569249676 569250498 822 False 854.000000 854 86.019000 1214 2023 1 chr5B.!!$F3 809
14 TraesCS1A01G393600 chr5B 569224138 569224840 702 False 584.000000 584 82.511000 678 1351 1 chr5B.!!$F2 673

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
874 1318 0.168128 ATAAACGAACCTTGCGCTGC 59.832 50.0 9.73 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 4904 0.178068 CATTCTGACGGACGGGGAAT 59.822 55.0 0.0 0.69 0.0 3.01 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 2.978824 TCGCAGCACTACCCTTCC 59.021 61.111 0.00 0.00 0.00 3.46
40 41 1.067495 CACCTTTCTCTCCGTGTCTCC 60.067 57.143 0.00 0.00 0.00 3.71
47 48 1.972223 CTCCGTGTCTCCAGACCGT 60.972 63.158 4.25 0.00 44.15 4.83
48 49 2.201436 CTCCGTGTCTCCAGACCGTG 62.201 65.000 4.25 3.20 44.15 4.94
51 52 1.069090 GTGTCTCCAGACCGTGCAA 59.931 57.895 4.25 0.00 44.15 4.08
54 55 1.078759 GTCTCCAGACCGTGCAATCG 61.079 60.000 0.00 0.00 39.07 3.34
73 74 2.168521 TCGGAGTTGATCTTGACCCATC 59.831 50.000 0.00 0.00 0.00 3.51
74 75 2.169352 CGGAGTTGATCTTGACCCATCT 59.831 50.000 0.00 0.00 0.00 2.90
80 81 4.412796 TGATCTTGACCCATCTGTCATC 57.587 45.455 0.00 0.00 44.27 2.92
106 107 1.479709 CTCCCACTTCTGGTCGATCT 58.520 55.000 0.00 0.00 35.46 2.75
114 115 2.738587 TCTGGTCGATCTTAGGCTCT 57.261 50.000 0.00 0.00 0.00 4.09
120 121 2.166664 GTCGATCTTAGGCTCTGGTTGT 59.833 50.000 0.00 0.00 0.00 3.32
162 163 1.003355 CTTCCACTCGGCCATGTGT 60.003 57.895 19.61 2.48 32.76 3.72
189 190 7.788026 ACCTTACCGTAGTCAATATTTCATGA 58.212 34.615 0.00 0.00 0.00 3.07
193 194 4.452455 CCGTAGTCAATATTTCATGAGGCC 59.548 45.833 0.00 0.00 0.00 5.19
198 202 4.999950 GTCAATATTTCATGAGGCCGATCT 59.000 41.667 0.00 0.00 0.00 2.75
205 209 0.761802 ATGAGGCCGATCTTCTTCCC 59.238 55.000 0.00 0.00 0.00 3.97
213 217 2.480416 CCGATCTTCTTCCCGTCTCTTG 60.480 54.545 0.00 0.00 0.00 3.02
218 222 1.266178 TCTTCCCGTCTCTTGCATCA 58.734 50.000 0.00 0.00 0.00 3.07
220 224 2.159043 TCTTCCCGTCTCTTGCATCATC 60.159 50.000 0.00 0.00 0.00 2.92
221 225 0.465705 TCCCGTCTCTTGCATCATCC 59.534 55.000 0.00 0.00 0.00 3.51
222 226 0.877649 CCCGTCTCTTGCATCATCCG 60.878 60.000 0.00 0.00 0.00 4.18
223 227 0.877649 CCGTCTCTTGCATCATCCGG 60.878 60.000 0.00 0.00 0.00 5.14
263 279 3.505680 CCATAGTCTCCTTCTCCTCATCG 59.494 52.174 0.00 0.00 0.00 3.84
264 280 2.065899 AGTCTCCTTCTCCTCATCGG 57.934 55.000 0.00 0.00 0.00 4.18
266 282 0.757188 TCTCCTTCTCCTCATCGGCC 60.757 60.000 0.00 0.00 0.00 6.13
271 287 2.852495 TTCTCCTCATCGGCCGCAAC 62.852 60.000 23.51 0.00 0.00 4.17
286 302 1.890041 CAACGGCGAACCAGTCCAA 60.890 57.895 16.62 0.00 34.57 3.53
310 326 1.306226 AGGAGGCTAGGGCGTTCTT 60.306 57.895 0.00 0.00 38.87 2.52
312 328 1.153349 GAGGCTAGGGCGTTCTTGG 60.153 63.158 0.00 0.00 39.81 3.61
344 363 2.597510 GGCAGGGTCACCACAACC 60.598 66.667 0.00 0.00 40.13 3.77
353 372 1.418637 GTCACCACAACCCCTAACTCA 59.581 52.381 0.00 0.00 0.00 3.41
365 384 2.416547 CCCTAACTCAGAACGCAACATG 59.583 50.000 0.00 0.00 0.00 3.21
370 389 2.115052 AGAACGCAACATGCCCCA 59.885 55.556 0.00 0.00 41.12 4.96
371 390 1.973281 AGAACGCAACATGCCCCAG 60.973 57.895 0.00 0.00 41.12 4.45
372 391 1.971167 GAACGCAACATGCCCCAGA 60.971 57.895 0.00 0.00 41.12 3.86
373 392 1.523154 GAACGCAACATGCCCCAGAA 61.523 55.000 0.00 0.00 41.12 3.02
374 393 1.805428 AACGCAACATGCCCCAGAAC 61.805 55.000 0.00 0.00 41.12 3.01
376 395 2.568090 CAACATGCCCCAGAACGC 59.432 61.111 0.00 0.00 0.00 4.84
378 397 1.530419 AACATGCCCCAGAACGCAA 60.530 52.632 0.00 0.00 38.75 4.85
379 398 1.805428 AACATGCCCCAGAACGCAAC 61.805 55.000 0.00 0.00 38.75 4.17
380 399 2.115052 ATGCCCCAGAACGCAACA 59.885 55.556 0.00 0.00 38.75 3.33
381 400 2.268076 ATGCCCCAGAACGCAACAC 61.268 57.895 0.00 0.00 38.75 3.32
398 440 1.977009 ACGCACCATCGTCTCCTCA 60.977 57.895 0.00 0.00 38.44 3.86
465 507 0.540830 AAGAGCTGAGACCTGACCGT 60.541 55.000 0.00 0.00 0.00 4.83
467 509 2.179517 GCTGAGACCTGACCGTCG 59.820 66.667 0.00 0.00 37.85 5.12
493 535 3.487942 CGTTTCGTATCATTCGCCACATA 59.512 43.478 0.00 0.00 0.00 2.29
511 553 4.581824 CACATATGTATCTTGGCCTTTGCT 59.418 41.667 8.32 0.00 37.74 3.91
535 577 2.742372 CTCGTTTCCCACAGGGCG 60.742 66.667 0.00 0.00 43.94 6.13
579 625 4.200283 GCTCGAGGACTCCGGCTG 62.200 72.222 15.58 0.00 0.00 4.85
593 639 2.753029 GCTGTCAGGTCCTTGCCT 59.247 61.111 1.14 0.00 39.99 4.75
602 648 4.522789 GTCAGGTCCTTGCCTTATTCAAAA 59.477 41.667 0.00 0.00 36.58 2.44
608 654 4.466015 TCCTTGCCTTATTCAAAACCATCC 59.534 41.667 0.00 0.00 0.00 3.51
613 659 4.440663 GCCTTATTCAAAACCATCCTGAGC 60.441 45.833 0.00 0.00 0.00 4.26
635 681 3.877559 TGATAGGCAGATTTCACACTGG 58.122 45.455 0.00 0.00 35.05 4.00
641 687 4.411540 AGGCAGATTTCACACTGGAGATAT 59.588 41.667 0.00 0.00 35.05 1.63
658 704 6.316140 TGGAGATATCATTTTTGTCTGGTTCG 59.684 38.462 5.32 0.00 0.00 3.95
662 708 4.159377 TCATTTTTGTCTGGTTCGATGC 57.841 40.909 0.00 0.00 0.00 3.91
772 1195 3.740397 CGGTGAGCGGTGGTACGA 61.740 66.667 0.00 0.00 35.47 3.43
796 1223 4.022464 GTCCATGTGACAAAACAAACGA 57.978 40.909 8.84 0.00 43.85 3.85
798 1225 5.753744 GTCCATGTGACAAAACAAACGATA 58.246 37.500 8.84 0.00 43.85 2.92
799 1226 6.378582 GTCCATGTGACAAAACAAACGATAT 58.621 36.000 8.84 0.00 43.85 1.63
800 1227 7.523219 GTCCATGTGACAAAACAAACGATATA 58.477 34.615 8.84 0.00 43.85 0.86
803 1230 7.643764 CCATGTGACAAAACAAACGATATATCC 59.356 37.037 7.15 0.00 32.81 2.59
804 1231 7.674471 TGTGACAAAACAAACGATATATCCA 57.326 32.000 7.15 0.00 0.00 3.41
805 1232 8.100508 TGTGACAAAACAAACGATATATCCAA 57.899 30.769 7.15 0.00 0.00 3.53
807 1234 8.234546 GTGACAAAACAAACGATATATCCAACT 58.765 33.333 7.15 0.00 0.00 3.16
808 1235 8.788806 TGACAAAACAAACGATATATCCAACTT 58.211 29.630 7.15 0.00 0.00 2.66
809 1236 9.620660 GACAAAACAAACGATATATCCAACTTT 57.379 29.630 7.15 0.00 0.00 2.66
810 1237 9.620660 ACAAAACAAACGATATATCCAACTTTC 57.379 29.630 7.15 0.00 0.00 2.62
811 1238 9.840427 CAAAACAAACGATATATCCAACTTTCT 57.160 29.630 7.15 0.00 0.00 2.52
867 1311 7.274447 TCCCAAACGATATATAAACGAACCTT 58.726 34.615 15.91 1.95 0.00 3.50
868 1312 7.225145 TCCCAAACGATATATAAACGAACCTTG 59.775 37.037 15.91 12.64 0.00 3.61
874 1318 0.168128 ATAAACGAACCTTGCGCTGC 59.832 50.000 9.73 0.00 0.00 5.25
880 1342 2.988942 GAACCTTGCGCTGCACACAC 62.989 60.000 9.73 0.00 38.71 3.82
885 1347 4.612536 GCGCTGCACACACCACAC 62.613 66.667 0.00 0.00 0.00 3.82
902 1364 3.583806 CACACAAAGCACAAAAGAACCA 58.416 40.909 0.00 0.00 0.00 3.67
913 1384 5.689068 GCACAAAAGAACCATCTTCTTCTTG 59.311 40.000 11.77 11.77 45.19 3.02
914 1385 6.681368 GCACAAAAGAACCATCTTCTTCTTGT 60.681 38.462 12.53 12.53 45.19 3.16
915 1386 7.260603 CACAAAAGAACCATCTTCTTCTTGTT 58.739 34.615 14.16 0.00 45.19 2.83
916 1387 7.221452 CACAAAAGAACCATCTTCTTCTTGTTG 59.779 37.037 14.16 9.81 45.19 3.33
917 1388 7.093771 ACAAAAGAACCATCTTCTTCTTGTTGT 60.094 33.333 12.53 9.32 45.19 3.32
918 1389 7.410120 AAAGAACCATCTTCTTCTTGTTGTT 57.590 32.000 0.00 0.00 45.19 2.83
919 1390 6.382869 AGAACCATCTTCTTCTTGTTGTTG 57.617 37.500 0.00 0.00 29.15 3.33
956 1438 2.334023 ACCAGTCCAAGAAGAAGAGCT 58.666 47.619 0.00 0.00 0.00 4.09
1303 1793 2.257371 CGTGCGAGAAGAACCGGA 59.743 61.111 9.46 0.00 0.00 5.14
1554 3216 7.179927 GAGGTTAAAGCTCGATTAATCTTCC 57.820 40.000 13.45 1.66 34.64 3.46
1666 4883 4.210746 CACATTCGATCGATCTGCTTGAAT 59.789 41.667 20.18 18.47 0.00 2.57
1675 4893 4.082787 TCGATCTGCTTGAATGTTTTTCCC 60.083 41.667 0.00 0.00 0.00 3.97
1681 4899 3.005367 GCTTGAATGTTTTTCCCCTTCGA 59.995 43.478 0.00 0.00 0.00 3.71
1686 4904 1.161843 GTTTTTCCCCTTCGATGCGA 58.838 50.000 0.00 0.00 0.00 5.10
1779 5009 5.715070 CTTCAGTTTTCTACCTGATCGACT 58.285 41.667 0.00 0.00 0.00 4.18
1792 5023 1.874231 GATCGACTAGACGAGCCATGA 59.126 52.381 19.62 0.00 45.22 3.07
1797 5028 0.029567 CTAGACGAGCCATGACCGAC 59.970 60.000 0.00 0.00 0.00 4.79
1827 5068 2.307309 CGCCGTCTGTTGCTTTCGA 61.307 57.895 0.00 0.00 0.00 3.71
1865 5312 1.136141 CACGTGCAGAAACATGAGAGC 60.136 52.381 0.82 0.00 0.00 4.09
1873 5320 4.260132 GCAGAAACATGAGAGCTTGATACG 60.260 45.833 0.00 0.00 0.00 3.06
1900 5348 0.321564 CATGCTCACCCGTGGAGAAA 60.322 55.000 0.00 0.00 34.24 2.52
1914 5362 7.120726 ACCCGTGGAGAAATTTGTTTAGATAAG 59.879 37.037 0.00 0.00 0.00 1.73
1970 5423 5.041191 AGTCACTCAAAGATTTGTGTCCT 57.959 39.130 9.41 6.69 41.35 3.85
2182 6165 2.025727 CGTACACGGCGGAGATCC 59.974 66.667 13.24 0.00 35.37 3.36
2186 6169 0.753848 TACACGGCGGAGATCCATCA 60.754 55.000 13.24 0.00 35.14 3.07
2188 6171 0.461870 CACGGCGGAGATCCATCAAA 60.462 55.000 13.24 0.00 35.14 2.69
2191 6174 1.811558 CGGCGGAGATCCATCAAACAT 60.812 52.381 0.00 0.00 35.14 2.71
2199 6182 6.128090 CGGAGATCCATCAAACATAATCATGG 60.128 42.308 0.00 0.00 34.25 3.66
2203 6186 4.036616 TCCATCAAACATAATCATGGCACG 59.963 41.667 0.00 0.00 36.39 5.34
2206 6189 3.065233 TCAAACATAATCATGGCACGCTC 59.935 43.478 0.00 0.00 36.39 5.03
2289 6279 5.532406 ACCAAAGTATTCAATCATGGATCGG 59.468 40.000 0.00 0.00 0.00 4.18
2347 6337 6.564125 CGATCAACAACTACTCCAGTCAAAAC 60.564 42.308 0.00 0.00 36.04 2.43
2375 6365 3.595819 GCCGCTTGCTTTGGAGAT 58.404 55.556 0.00 0.00 36.87 2.75
2383 6373 2.760634 TGCTTTGGAGATAGCGACAA 57.239 45.000 0.00 0.00 40.26 3.18
2384 6374 3.052455 TGCTTTGGAGATAGCGACAAA 57.948 42.857 0.00 3.74 40.26 2.83
2385 6375 3.407698 TGCTTTGGAGATAGCGACAAAA 58.592 40.909 5.03 0.00 40.26 2.44
2386 6376 4.009675 TGCTTTGGAGATAGCGACAAAAT 58.990 39.130 5.03 0.00 40.26 1.82
2387 6377 5.182487 TGCTTTGGAGATAGCGACAAAATA 58.818 37.500 5.03 0.00 40.26 1.40
2388 6378 5.822519 TGCTTTGGAGATAGCGACAAAATAT 59.177 36.000 5.03 0.00 40.26 1.28
2389 6379 6.989759 TGCTTTGGAGATAGCGACAAAATATA 59.010 34.615 5.03 0.00 40.26 0.86
2390 6380 7.171508 TGCTTTGGAGATAGCGACAAAATATAG 59.828 37.037 5.03 0.00 40.26 1.31
2391 6381 7.171678 GCTTTGGAGATAGCGACAAAATATAGT 59.828 37.037 5.03 0.00 33.04 2.12
2392 6382 9.692749 CTTTGGAGATAGCGACAAAATATAGTA 57.307 33.333 5.03 0.00 33.04 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.502130 GAGAAAGGTGGAGGAAGGGTAG 59.498 54.545 0.00 0.00 0.00 3.18
14 15 1.267121 CGGAGAGAAAGGTGGAGGAA 58.733 55.000 0.00 0.00 0.00 3.36
17 18 0.969894 ACACGGAGAGAAAGGTGGAG 59.030 55.000 0.00 0.00 34.78 3.86
47 48 3.002791 GTCAAGATCAACTCCGATTGCA 58.997 45.455 0.00 0.00 0.00 4.08
48 49 2.352960 GGTCAAGATCAACTCCGATTGC 59.647 50.000 0.00 0.00 0.00 3.56
51 52 2.187958 TGGGTCAAGATCAACTCCGAT 58.812 47.619 0.00 0.00 0.00 4.18
54 55 3.054802 ACAGATGGGTCAAGATCAACTCC 60.055 47.826 0.00 0.00 0.00 3.85
55 56 4.187694 GACAGATGGGTCAAGATCAACTC 58.812 47.826 0.00 0.00 37.73 3.01
73 74 3.866582 GGAGCCCCCGGATGACAG 61.867 72.222 0.73 0.00 0.00 3.51
106 107 0.320421 GCGTCACAACCAGAGCCTAA 60.320 55.000 0.00 0.00 0.00 2.69
114 115 4.980805 GCGAGGGCGTCACAACCA 62.981 66.667 8.06 0.00 40.36 3.67
162 163 9.537192 CATGAAATATTGACTACGGTAAGGTTA 57.463 33.333 0.00 0.00 0.00 2.85
189 190 1.677637 GACGGGAAGAAGATCGGCCT 61.678 60.000 0.00 0.00 0.00 5.19
193 194 2.803451 CAAGAGACGGGAAGAAGATCG 58.197 52.381 0.00 0.00 0.00 3.69
198 202 1.623311 TGATGCAAGAGACGGGAAGAA 59.377 47.619 0.00 0.00 0.00 2.52
205 209 1.493950 GCCGGATGATGCAAGAGACG 61.494 60.000 5.05 0.00 0.00 4.18
213 217 2.357517 CTACGGGCCGGATGATGC 60.358 66.667 31.78 0.00 0.00 3.91
245 261 2.026905 GCCGATGAGGAGAAGGAGACT 61.027 57.143 0.00 0.00 45.00 3.24
271 287 1.890041 TTGTTGGACTGGTTCGCCG 60.890 57.895 0.00 0.00 41.18 6.46
286 302 2.301738 GCCCTAGCCTCCTGGTTGT 61.302 63.158 0.00 0.00 35.27 3.32
344 363 2.163818 TGTTGCGTTCTGAGTTAGGG 57.836 50.000 0.00 0.00 0.00 3.53
347 366 1.804151 GGCATGTTGCGTTCTGAGTTA 59.196 47.619 0.00 0.00 46.21 2.24
353 372 1.973281 CTGGGGCATGTTGCGTTCT 60.973 57.895 0.00 0.00 46.21 3.01
365 384 4.025401 CGTGTTGCGTTCTGGGGC 62.025 66.667 0.00 0.00 35.54 5.80
376 395 1.626654 GGAGACGATGGTGCGTGTTG 61.627 60.000 0.00 0.00 45.72 3.33
378 397 2.214181 GAGGAGACGATGGTGCGTGT 62.214 60.000 0.00 0.00 45.72 4.49
379 398 1.517257 GAGGAGACGATGGTGCGTG 60.517 63.158 0.00 0.00 45.72 5.34
381 400 1.517257 GTGAGGAGACGATGGTGCG 60.517 63.158 0.00 0.00 37.29 5.34
398 440 1.167155 TTTATGTTGTGTGCGGCCGT 61.167 50.000 28.70 5.57 0.00 5.68
441 483 2.165437 GTCAGGTCTCAGCTCTTTCGAT 59.835 50.000 0.00 0.00 0.00 3.59
443 485 1.403514 GGTCAGGTCTCAGCTCTTTCG 60.404 57.143 0.00 0.00 0.00 3.46
453 495 2.675772 ACCCGACGGTCAGGTCTC 60.676 66.667 13.94 0.00 38.28 3.36
465 507 2.792196 CGAATGATACGAAACGACCCGA 60.792 50.000 0.00 0.00 0.00 5.14
467 509 1.257155 GCGAATGATACGAAACGACCC 59.743 52.381 0.00 0.00 0.00 4.46
476 518 6.036470 AGATACATATGTGGCGAATGATACG 58.964 40.000 18.81 0.00 0.00 3.06
493 535 2.291800 ACCAGCAAAGGCCAAGATACAT 60.292 45.455 5.01 0.00 42.56 2.29
511 553 1.525077 GTGGGAAACGAGTGCACCA 60.525 57.895 14.63 0.00 0.00 4.17
535 577 6.073222 CGGTTAACAAGCACAAGGGATATATC 60.073 42.308 8.10 3.96 0.00 1.63
549 591 0.992802 CTCGAGCTCGGTTAACAAGC 59.007 55.000 33.98 19.27 40.29 4.01
579 625 3.350219 TGAATAAGGCAAGGACCTGAC 57.650 47.619 0.00 0.00 39.93 3.51
593 639 5.569355 TCAGCTCAGGATGGTTTTGAATAA 58.431 37.500 0.00 0.00 36.16 1.40
602 648 1.055040 GCCTATCAGCTCAGGATGGT 58.945 55.000 9.30 0.00 36.16 3.55
608 654 3.808726 GTGAAATCTGCCTATCAGCTCAG 59.191 47.826 0.00 0.00 42.56 3.35
613 659 3.875727 CCAGTGTGAAATCTGCCTATCAG 59.124 47.826 0.00 0.00 44.21 2.90
635 681 7.539712 TCGAACCAGACAAAAATGATATCTC 57.460 36.000 3.98 0.00 0.00 2.75
641 687 3.057596 GGCATCGAACCAGACAAAAATGA 60.058 43.478 3.08 0.00 0.00 2.57
658 704 5.982356 TGCTACTGAGGATTATATGGCATC 58.018 41.667 1.65 0.00 0.00 3.91
662 708 5.674052 AGCTGCTACTGAGGATTATATGG 57.326 43.478 0.00 0.00 0.00 2.74
795 1222 6.075519 CGCGCGTATAGAAAGTTGGATATATC 60.076 42.308 24.19 3.96 0.00 1.63
796 1223 5.742453 CGCGCGTATAGAAAGTTGGATATAT 59.258 40.000 24.19 0.00 0.00 0.86
798 1225 3.918591 CGCGCGTATAGAAAGTTGGATAT 59.081 43.478 24.19 0.00 0.00 1.63
799 1226 3.003585 TCGCGCGTATAGAAAGTTGGATA 59.996 43.478 30.98 0.00 0.00 2.59
800 1227 2.124903 CGCGCGTATAGAAAGTTGGAT 58.875 47.619 24.19 0.00 0.00 3.41
803 1230 2.447250 TCTCGCGCGTATAGAAAGTTG 58.553 47.619 30.98 6.51 0.00 3.16
804 1231 2.717530 CTCTCGCGCGTATAGAAAGTT 58.282 47.619 30.98 0.00 0.00 2.66
805 1232 1.597445 GCTCTCGCGCGTATAGAAAGT 60.597 52.381 30.98 0.00 0.00 2.66
807 1234 0.317603 GGCTCTCGCGCGTATAGAAA 60.318 55.000 30.98 7.39 36.88 2.52
808 1235 1.281960 GGCTCTCGCGCGTATAGAA 59.718 57.895 30.98 8.24 36.88 2.10
809 1236 2.944429 GGCTCTCGCGCGTATAGA 59.056 61.111 30.98 23.33 36.88 1.98
810 1237 2.499944 CGGCTCTCGCGCGTATAG 60.500 66.667 30.98 24.02 36.88 1.31
811 1238 2.951315 CTCGGCTCTCGCGCGTATA 61.951 63.158 30.98 15.09 39.05 1.47
812 1239 4.315122 CTCGGCTCTCGCGCGTAT 62.315 66.667 30.98 0.00 39.05 3.06
874 1318 0.525311 TGTGCTTTGTGTGGTGTGTG 59.475 50.000 0.00 0.00 0.00 3.82
880 1342 2.929398 GGTTCTTTTGTGCTTTGTGTGG 59.071 45.455 0.00 0.00 0.00 4.17
884 1346 5.127682 AGAAGATGGTTCTTTTGTGCTTTGT 59.872 36.000 0.00 0.00 42.34 2.83
885 1347 5.594926 AGAAGATGGTTCTTTTGTGCTTTG 58.405 37.500 0.00 0.00 42.34 2.77
902 1364 7.872113 AGAAGAACAACAACAAGAAGAAGAT 57.128 32.000 0.00 0.00 0.00 2.40
956 1438 1.203052 CTACCTAGAAAACCACGGCGA 59.797 52.381 16.62 0.00 0.00 5.54
1017 1501 4.320456 CAGCTCACCACCACCGCT 62.320 66.667 0.00 0.00 0.00 5.52
1050 1534 4.135153 CCGGTGCACTCCTCCTCG 62.135 72.222 17.98 9.58 0.00 4.63
1297 1787 1.885163 GACGATGAGGTGGTCCGGTT 61.885 60.000 0.00 0.00 39.05 4.44
1303 1793 1.304217 ACGAGGACGATGAGGTGGT 60.304 57.895 0.00 0.00 42.66 4.16
1383 1961 1.134580 CAGACATCAACTCAGGCGGAT 60.135 52.381 0.00 0.00 0.00 4.18
1514 3075 3.790152 ACCTCGTATAGTTTCCGGAAC 57.210 47.619 18.64 12.36 38.58 3.62
1554 3216 3.906218 TGGGTAGATCAAGATCCTCATGG 59.094 47.826 6.45 0.00 38.58 3.66
1666 4883 0.878416 CGCATCGAAGGGGAAAAACA 59.122 50.000 0.00 0.00 0.00 2.83
1675 4893 1.956170 CGGGGAATCGCATCGAAGG 60.956 63.158 0.00 0.00 39.99 3.46
1681 4899 3.441011 GACGGACGGGGAATCGCAT 62.441 63.158 0.00 0.00 0.00 4.73
1686 4904 0.178068 CATTCTGACGGACGGGGAAT 59.822 55.000 0.00 0.69 0.00 3.01
1779 5009 1.381928 GGTCGGTCATGGCTCGTCTA 61.382 60.000 0.00 0.00 0.00 2.59
1827 5068 1.139058 GTGTGTTGAGGGCGAGGATAT 59.861 52.381 0.00 0.00 0.00 1.63
1865 5312 1.528586 GCATGCACTAGCCGTATCAAG 59.471 52.381 14.21 0.00 41.13 3.02
1873 5320 1.821332 GGGTGAGCATGCACTAGCC 60.821 63.158 21.98 19.17 41.13 3.93
1956 5409 4.210331 ACTTGCAGAGGACACAAATCTTT 58.790 39.130 0.00 0.00 0.00 2.52
1970 5423 4.237724 CGTCTATCAGACAAACTTGCAGA 58.762 43.478 7.08 0.00 45.30 4.26
2142 6123 3.980775 TGTGCGTGTACATATCATCATCG 59.019 43.478 0.00 0.00 0.00 3.84
2176 6159 6.208007 TGCCATGATTATGTTTGATGGATCTC 59.792 38.462 0.00 0.00 36.45 2.75
2182 6165 3.732219 GCGTGCCATGATTATGTTTGATG 59.268 43.478 0.00 0.00 32.21 3.07
2186 6169 2.358898 GGAGCGTGCCATGATTATGTTT 59.641 45.455 0.00 0.00 32.21 2.83
2188 6171 1.134128 TGGAGCGTGCCATGATTATGT 60.134 47.619 0.00 0.00 31.66 2.29
2191 6174 0.251634 TGTGGAGCGTGCCATGATTA 59.748 50.000 0.00 0.00 40.68 1.75
2199 6182 2.800096 CACAAAATGTGGAGCGTGC 58.200 52.632 2.56 0.00 44.27 5.34
2262 6252 7.307632 CGATCCATGATTGAATACTTTGGTCTC 60.308 40.741 0.00 0.00 0.00 3.36
2274 6264 2.771372 TGGAGACCGATCCATGATTGAA 59.229 45.455 0.00 0.00 44.56 2.69


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

AutoCloner maintained by Alex Coulton.