Multiple sequence alignment - TraesCS6D01G392100

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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 TraesCS6D01G392100 chr6D 100.000 2971 0 0 1 2971 466910192 466907222 0.000000e+00 5487
1 TraesCS6D01G392100 chr6A 93.474 2268 53 24 729 2971 613238284 613236087 0.000000e+00 3280
2 TraesCS6D01G392100 chr6A 91.575 546 7 5 2424 2969 613171575 613171069 0.000000e+00 717
3 TraesCS6D01G392100 chr6A 90.381 499 7 5 2471 2969 613153413 613152956 4.210000e-173 617
4 TraesCS6D01G392100 chr6A 85.338 607 52 12 44 616 613238979 613238376 7.090000e-166 593
5 TraesCS6D01G392100 chr6A 93.902 246 4 4 2726 2971 613190493 613190259 7.830000e-96 361
6 TraesCS6D01G392100 chr6A 100.000 119 0 0 2424 2542 613190682 613190564 1.390000e-53 220
7 TraesCS6D01G392100 chr6A 98.400 125 1 1 2848 2971 613217949 613217825 4.990000e-53 219
8 TraesCS6D01G392100 chr6A 98.980 98 1 0 2424 2521 613153512 613153415 3.040000e-40 176
9 TraesCS6D01G392100 chr6B 88.358 2010 110 60 491 2443 712102861 712104803 0.000000e+00 2302
10 TraesCS6D01G392100 chr5D 78.285 548 106 11 1414 1956 37202141 37202680 1.020000e-89 340
11 TraesCS6D01G392100 chr5B 77.157 591 124 10 1371 1956 27813317 27813901 1.710000e-87 333
12 TraesCS6D01G392100 chr7A 77.778 558 111 11 1414 1963 31592124 31592676 6.140000e-87 331
13 TraesCS6D01G392100 chr3A 80.697 373 66 6 1416 1785 60029366 60028997 4.850000e-73 285
14 TraesCS6D01G392100 chr3D 79.839 372 71 4 1416 1785 47704120 47703751 4.880000e-68 268
15 TraesCS6D01G392100 chr3D 79.301 372 73 4 1416 1785 47708363 47707994 1.060000e-64 257
16 TraesCS6D01G392100 chr3B 79.893 373 69 6 1416 1785 74762565 74762934 4.880000e-68 268


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 TraesCS6D01G392100 chr6D 466907222 466910192 2970 True 5487.0 5487 100.0000 1 2971 1 chr6D.!!$R1 2970
1 TraesCS6D01G392100 chr6A 613236087 613238979 2892 True 1936.5 3280 89.4060 44 2971 2 chr6A.!!$R5 2927
2 TraesCS6D01G392100 chr6A 613171069 613171575 506 True 717.0 717 91.5750 2424 2969 1 chr6A.!!$R1 545
3 TraesCS6D01G392100 chr6A 613152956 613153512 556 True 396.5 617 94.6805 2424 2969 2 chr6A.!!$R3 545
4 TraesCS6D01G392100 chr6B 712102861 712104803 1942 False 2302.0 2302 88.3580 491 2443 1 chr6B.!!$F1 1952
5 TraesCS6D01G392100 chr5D 37202141 37202680 539 False 340.0 340 78.2850 1414 1956 1 chr5D.!!$F1 542
6 TraesCS6D01G392100 chr5B 27813317 27813901 584 False 333.0 333 77.1570 1371 1956 1 chr5B.!!$F1 585
7 TraesCS6D01G392100 chr7A 31592124 31592676 552 False 331.0 331 77.7780 1414 1963 1 chr7A.!!$F1 549
8 TraesCS6D01G392100 chr3D 47703751 47708363 4612 True 262.5 268 79.5700 1416 1785 2 chr3D.!!$R1 369

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
631 667 0.106769 TTGGAAGCACAACAGAGGCA 60.107 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 3211 2.401583 ACGCATCCATACAAAGCTCA 57.598 45.0 0.0 0.0 0.0 4.26 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
42 43 7.979444 TTTTTGGAAAGTACTCATACTCTGG 57.021 36.000 0.00 0.00 41.00 3.86
51 52 8.553459 AAGTACTCATACTCTGGAAAAATGTG 57.447 34.615 0.00 0.00 41.00 3.21
65 66 9.934190 CTGGAAAAATGTGTTTGGAAATAAAAG 57.066 29.630 0.00 0.00 0.00 2.27
73 75 7.262048 TGTGTTTGGAAATAAAAGTTCCTCAC 58.738 34.615 7.56 12.35 44.24 3.51
74 76 7.123547 TGTGTTTGGAAATAAAAGTTCCTCACT 59.876 33.333 19.04 0.00 44.24 3.41
90 92 7.391833 AGTTCCTCACTTCTATGAAAATGTTCC 59.608 37.037 0.00 0.00 28.64 3.62
95 97 4.396166 ACTTCTATGAAAATGTTCCCAGCG 59.604 41.667 0.00 0.00 32.28 5.18
102 104 1.600023 AATGTTCCCAGCGAAAACGA 58.400 45.000 0.00 0.00 30.39 3.85
137 139 8.670521 ATTAAATCAAATCAGGAAGGGTTCTT 57.329 30.769 0.00 0.00 35.62 2.52
146 148 3.418684 GGAAGGGTTCTTGCTAGTTGA 57.581 47.619 0.00 0.00 38.17 3.18
149 151 1.002087 AGGGTTCTTGCTAGTTGACCG 59.998 52.381 10.11 0.00 0.00 4.79
153 155 2.047655 TTGCTAGTTGACCGGCCG 60.048 61.111 21.04 21.04 0.00 6.13
160 162 2.030958 GTTGACCGGCCGAATCGTT 61.031 57.895 30.73 2.44 0.00 3.85
162 164 0.176219 TTGACCGGCCGAATCGTTAT 59.824 50.000 30.73 0.23 0.00 1.89
165 167 1.788886 GACCGGCCGAATCGTTATTAC 59.211 52.381 30.73 0.00 0.00 1.89
178 180 2.596575 CGTTATTACGCGCAATGACAGG 60.597 50.000 22.14 7.40 41.41 4.00
179 181 2.303163 TATTACGCGCAATGACAGGT 57.697 45.000 14.79 0.00 0.00 4.00
180 182 1.448985 ATTACGCGCAATGACAGGTT 58.551 45.000 5.73 0.00 0.00 3.50
182 184 2.081725 TACGCGCAATGACAGGTTTA 57.918 45.000 5.73 0.00 0.00 2.01
188 190 3.611530 GCGCAATGACAGGTTTACATGTT 60.612 43.478 2.30 0.00 41.31 2.71
189 191 4.378978 GCGCAATGACAGGTTTACATGTTA 60.379 41.667 2.30 0.00 41.31 2.41
190 192 5.323900 CGCAATGACAGGTTTACATGTTAG 58.676 41.667 2.30 0.00 41.31 2.34
206 208 6.151049 ACATGTTAGTACCTCCCTATCCATT 58.849 40.000 0.00 0.00 0.00 3.16
249 251 3.194968 TCAACCGATCTCCTCCTTACAAC 59.805 47.826 0.00 0.00 0.00 3.32
251 253 2.022195 CCGATCTCCTCCTTACAACGA 58.978 52.381 0.00 0.00 0.00 3.85
255 257 5.047943 CCGATCTCCTCCTTACAACGATTAT 60.048 44.000 0.00 0.00 0.00 1.28
266 268 9.661563 TCCTTACAACGATTATTTTATGTCAGT 57.338 29.630 0.00 0.00 0.00 3.41
281 283 2.716398 GTCAGTTGTTGACGCCTTTTC 58.284 47.619 0.00 0.00 46.13 2.29
284 286 2.354510 CAGTTGTTGACGCCTTTTCTGA 59.645 45.455 0.00 0.00 0.00 3.27
303 305 9.677567 TTTTCTGAAAAAGATAAATCCTGAACG 57.322 29.630 12.85 0.00 33.93 3.95
305 307 8.391075 TCTGAAAAAGATAAATCCTGAACGTT 57.609 30.769 0.00 0.00 0.00 3.99
307 309 7.590279 TGAAAAAGATAAATCCTGAACGTTCC 58.410 34.615 24.78 8.19 0.00 3.62
311 313 5.671493 AGATAAATCCTGAACGTTCCGATT 58.329 37.500 24.78 24.49 30.82 3.34
312 314 6.812998 AGATAAATCCTGAACGTTCCGATTA 58.187 36.000 27.52 19.57 29.98 1.75
313 315 6.924060 AGATAAATCCTGAACGTTCCGATTAG 59.076 38.462 27.52 18.34 29.98 1.73
335 337 2.427095 GCCCATAGCAAATCGAAGGTTT 59.573 45.455 0.00 0.00 42.97 3.27
339 341 6.033966 CCCATAGCAAATCGAAGGTTTTTAC 58.966 40.000 0.00 0.00 0.00 2.01
340 342 5.737290 CCATAGCAAATCGAAGGTTTTTACG 59.263 40.000 0.00 0.00 0.00 3.18
342 344 4.779987 AGCAAATCGAAGGTTTTTACGAC 58.220 39.130 0.00 0.00 37.58 4.34
367 369 5.316167 ACTTTAGTTGATGCAAGGATGACA 58.684 37.500 0.00 0.00 0.00 3.58
372 374 2.715046 TGATGCAAGGATGACAGGTTC 58.285 47.619 0.00 0.00 0.00 3.62
375 377 2.229792 TGCAAGGATGACAGGTTCAAC 58.770 47.619 0.00 0.00 37.92 3.18
400 402 1.549203 AGCATGGCGAATTTGTCCTT 58.451 45.000 0.00 0.00 0.00 3.36
401 403 1.474077 AGCATGGCGAATTTGTCCTTC 59.526 47.619 0.00 0.00 0.00 3.46
403 405 2.733227 GCATGGCGAATTTGTCCTTCTG 60.733 50.000 0.00 0.00 0.00 3.02
435 445 0.881796 GCAACTAAGCTTGACACCCC 59.118 55.000 9.86 0.00 0.00 4.95
481 493 4.622260 AAAGTTTGATTTGTCATGGGGG 57.378 40.909 0.00 0.00 0.00 5.40
483 495 3.165071 AGTTTGATTTGTCATGGGGGAC 58.835 45.455 0.00 0.00 38.29 4.46
484 496 1.832883 TTGATTTGTCATGGGGGACG 58.167 50.000 0.00 0.00 40.72 4.79
486 498 1.074727 TGATTTGTCATGGGGGACGTT 59.925 47.619 0.00 0.00 40.72 3.99
487 499 2.167662 GATTTGTCATGGGGGACGTTT 58.832 47.619 0.00 0.00 40.72 3.60
488 500 2.074729 TTTGTCATGGGGGACGTTTT 57.925 45.000 0.00 0.00 40.72 2.43
600 636 1.985116 GAGTCCTTGGCCTCGGTCT 60.985 63.158 3.32 7.34 0.00 3.85
616 652 0.840722 GTCTGGTCCCTTCCCTTGGA 60.841 60.000 0.00 0.00 0.00 3.53
625 661 3.913855 TTCCCTTGGAAGCACAACA 57.086 47.368 0.00 0.00 36.71 3.33
626 662 1.691196 TTCCCTTGGAAGCACAACAG 58.309 50.000 0.00 0.00 36.71 3.16
627 663 0.843309 TCCCTTGGAAGCACAACAGA 59.157 50.000 0.00 0.00 0.00 3.41
628 664 1.202806 TCCCTTGGAAGCACAACAGAG 60.203 52.381 0.00 0.00 0.00 3.35
629 665 1.242076 CCTTGGAAGCACAACAGAGG 58.758 55.000 0.00 0.00 0.00 3.69
630 666 0.595095 CTTGGAAGCACAACAGAGGC 59.405 55.000 0.00 0.00 0.00 4.70
631 667 0.106769 TTGGAAGCACAACAGAGGCA 60.107 50.000 0.00 0.00 0.00 4.75
632 668 0.111061 TGGAAGCACAACAGAGGCAT 59.889 50.000 0.00 0.00 0.00 4.40
633 669 0.807496 GGAAGCACAACAGAGGCATC 59.193 55.000 0.00 0.00 0.00 3.91
634 670 1.527034 GAAGCACAACAGAGGCATCA 58.473 50.000 0.00 0.00 0.00 3.07
635 671 1.467734 GAAGCACAACAGAGGCATCAG 59.532 52.381 0.00 0.00 0.00 2.90
636 672 0.322277 AGCACAACAGAGGCATCAGG 60.322 55.000 0.00 0.00 0.00 3.86
637 673 1.930908 GCACAACAGAGGCATCAGGC 61.931 60.000 0.00 0.00 43.74 4.85
648 684 1.773054 GCATCAGGCATGAGACGCTG 61.773 60.000 7.33 0.42 43.97 5.18
653 689 2.109126 GGCATGAGACGCTGGGTTC 61.109 63.158 0.00 0.09 0.00 3.62
668 704 3.672447 TTCGTGGCCAGCGACGTA 61.672 61.111 23.93 13.71 45.77 3.57
669 705 3.620300 TTCGTGGCCAGCGACGTAG 62.620 63.158 23.93 0.00 45.77 3.51
690 754 2.274437 CGCACCGAGTGTAGTCTAGTA 58.726 52.381 6.02 0.00 35.75 1.82
691 755 2.284684 CGCACCGAGTGTAGTCTAGTAG 59.715 54.545 6.02 0.00 35.75 2.57
692 756 3.269178 GCACCGAGTGTAGTCTAGTAGT 58.731 50.000 0.00 0.00 35.75 2.73
694 758 4.757594 CACCGAGTGTAGTCTAGTAGTCT 58.242 47.826 2.46 2.46 0.00 3.24
695 759 5.680922 GCACCGAGTGTAGTCTAGTAGTCTA 60.681 48.000 0.58 0.58 35.75 2.59
696 760 5.978919 CACCGAGTGTAGTCTAGTAGTCTAG 59.021 48.000 4.60 0.00 43.48 2.43
697 761 5.656416 ACCGAGTGTAGTCTAGTAGTCTAGT 59.344 44.000 4.60 0.00 42.88 2.57
698 762 5.978919 CCGAGTGTAGTCTAGTAGTCTAGTG 59.021 48.000 4.60 0.00 42.88 2.74
699 763 6.405731 CCGAGTGTAGTCTAGTAGTCTAGTGT 60.406 46.154 4.60 0.00 42.88 3.55
700 764 7.201776 CCGAGTGTAGTCTAGTAGTCTAGTGTA 60.202 44.444 4.60 0.00 42.88 2.90
701 765 7.643764 CGAGTGTAGTCTAGTAGTCTAGTGTAC 59.356 44.444 4.60 3.42 42.88 2.90
702 766 7.479980 AGTGTAGTCTAGTAGTCTAGTGTACG 58.520 42.308 4.60 0.00 42.88 3.67
703 767 6.198216 GTGTAGTCTAGTAGTCTAGTGTACGC 59.802 46.154 4.60 0.00 42.88 4.42
704 768 5.336150 AGTCTAGTAGTCTAGTGTACGCA 57.664 43.478 9.48 0.00 42.88 5.24
705 769 5.108517 AGTCTAGTAGTCTAGTGTACGCAC 58.891 45.833 9.48 0.00 42.88 5.34
706 770 4.269844 GTCTAGTAGTCTAGTGTACGCACC 59.730 50.000 9.48 0.00 46.35 5.01
707 771 2.005451 AGTAGTCTAGTGTACGCACCG 58.995 52.381 9.48 0.00 46.35 4.94
708 772 0.729116 TAGTCTAGTGTACGCACCGC 59.271 55.000 9.48 0.00 46.35 5.68
710 774 2.578713 CTAGTGTACGCACCGCCG 60.579 66.667 9.48 0.00 46.35 6.46
741 819 3.243336 CGATAAGTATAACGGCCAGCTC 58.757 50.000 2.24 0.00 0.00 4.09
742 820 3.586892 GATAAGTATAACGGCCAGCTCC 58.413 50.000 2.24 0.00 0.00 4.70
743 821 1.200519 AAGTATAACGGCCAGCTCCA 58.799 50.000 2.24 0.00 0.00 3.86
744 822 0.753262 AGTATAACGGCCAGCTCCAG 59.247 55.000 2.24 0.00 0.00 3.86
745 823 0.880718 GTATAACGGCCAGCTCCAGC 60.881 60.000 2.24 0.00 42.49 4.85
777 855 5.804979 CGTGATTCCAAAACATAAATGGACC 59.195 40.000 0.00 0.00 42.71 4.46
779 857 5.478679 TGATTCCAAAACATAAATGGACCGT 59.521 36.000 0.00 0.00 42.71 4.83
849 927 2.743938 CCGCATTATAGAAGACGCTGT 58.256 47.619 0.00 0.00 0.00 4.40
1158 1248 0.768221 ACAAGGGGCAGGAGTTCTCA 60.768 55.000 2.24 0.00 0.00 3.27
1288 1383 2.079158 TCACCTCCTTCTACGTACGTG 58.921 52.381 30.25 19.22 0.00 4.49
1294 1398 3.614092 TCCTTCTACGTACGTGATCCTT 58.386 45.455 30.25 4.23 0.00 3.36
1301 1405 4.516365 ACGTACGTGATCCTTTTCTTCT 57.484 40.909 22.14 0.00 0.00 2.85
1304 1408 5.756833 ACGTACGTGATCCTTTTCTTCTTTT 59.243 36.000 22.14 0.00 0.00 2.27
1306 1410 6.073980 CGTACGTGATCCTTTTCTTCTTTTCA 60.074 38.462 7.22 0.00 0.00 2.69
1307 1411 6.061231 ACGTGATCCTTTTCTTCTTTTCAC 57.939 37.500 0.00 0.00 0.00 3.18
1308 1412 5.823045 ACGTGATCCTTTTCTTCTTTTCACT 59.177 36.000 0.00 0.00 32.19 3.41
1309 1413 6.318900 ACGTGATCCTTTTCTTCTTTTCACTT 59.681 34.615 0.00 0.00 32.19 3.16
1310 1414 7.148069 ACGTGATCCTTTTCTTCTTTTCACTTT 60.148 33.333 0.00 0.00 32.19 2.66
1311 1415 7.377131 CGTGATCCTTTTCTTCTTTTCACTTTC 59.623 37.037 0.00 0.00 32.19 2.62
1312 1416 8.190784 GTGATCCTTTTCTTCTTTTCACTTTCA 58.809 33.333 0.00 0.00 31.78 2.69
1313 1417 8.917088 TGATCCTTTTCTTCTTTTCACTTTCAT 58.083 29.630 0.00 0.00 0.00 2.57
1316 1420 8.624776 TCCTTTTCTTCTTTTCACTTTCATCTC 58.375 33.333 0.00 0.00 0.00 2.75
1318 1422 7.786178 TTTCTTCTTTTCACTTTCATCTCGA 57.214 32.000 0.00 0.00 0.00 4.04
1322 1426 4.687948 TCTTTTCACTTTCATCTCGAGCTG 59.312 41.667 10.02 10.02 0.00 4.24
1334 1438 1.612950 CTCGAGCTGTGCTGGATCTAT 59.387 52.381 0.00 0.00 42.04 1.98
1335 1439 2.034878 TCGAGCTGTGCTGGATCTATT 58.965 47.619 0.00 0.00 38.40 1.73
1337 1441 2.543012 CGAGCTGTGCTGGATCTATTTG 59.457 50.000 0.00 0.00 39.88 2.32
1343 1454 4.517285 TGTGCTGGATCTATTTGTTCTCC 58.483 43.478 0.00 0.00 0.00 3.71
1379 1490 6.639590 ATGGAAAATGGAAAATGGAATGGA 57.360 33.333 0.00 0.00 0.00 3.41
1380 1491 6.639590 TGGAAAATGGAAAATGGAATGGAT 57.360 33.333 0.00 0.00 0.00 3.41
1381 1492 6.416415 TGGAAAATGGAAAATGGAATGGATG 58.584 36.000 0.00 0.00 0.00 3.51
1383 1494 6.352910 GGAAAATGGAAAATGGAATGGATGGA 60.353 38.462 0.00 0.00 0.00 3.41
1481 1592 1.214367 ACGTGATGAACACCAACGTC 58.786 50.000 0.00 0.00 45.73 4.34
2647 5017 8.689069 GGACATACTTATATTTTCTCGTTCGAC 58.311 37.037 0.00 0.00 0.00 4.20
2650 5032 9.193133 CATACTTATATTTTCTCGTTCGACCAT 57.807 33.333 0.00 0.00 0.00 3.55
2727 5260 3.644861 AAAAAGTGGACCGGGCTAG 57.355 52.632 7.57 0.00 0.00 3.42
2736 5269 4.867599 CCGGGCTAGTTCGCGTCC 62.868 72.222 5.77 0.00 40.21 4.79
2783 5330 2.860009 CGAGCCCTCATGTACTACCTA 58.140 52.381 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.667107 CCAGAGTATGAGTACTTTCCAAAAATA 57.333 33.333 0.00 0.00 41.19 1.40
17 18 8.383175 TCCAGAGTATGAGTACTTTCCAAAAAT 58.617 33.333 0.00 0.00 41.19 1.82
18 19 7.741785 TCCAGAGTATGAGTACTTTCCAAAAA 58.258 34.615 0.00 0.00 41.19 1.94
19 20 7.311092 TCCAGAGTATGAGTACTTTCCAAAA 57.689 36.000 0.00 0.00 41.19 2.44
20 21 6.928348 TCCAGAGTATGAGTACTTTCCAAA 57.072 37.500 0.00 0.00 41.19 3.28
21 22 6.928348 TTCCAGAGTATGAGTACTTTCCAA 57.072 37.500 0.00 0.00 41.19 3.53
22 23 6.928348 TTTCCAGAGTATGAGTACTTTCCA 57.072 37.500 0.00 0.00 41.19 3.53
23 24 8.669243 CATTTTTCCAGAGTATGAGTACTTTCC 58.331 37.037 0.00 0.00 41.19 3.13
24 25 9.220767 ACATTTTTCCAGAGTATGAGTACTTTC 57.779 33.333 0.00 0.00 41.19 2.62
25 26 9.003658 CACATTTTTCCAGAGTATGAGTACTTT 57.996 33.333 0.00 0.00 41.19 2.66
26 27 8.157476 ACACATTTTTCCAGAGTATGAGTACTT 58.843 33.333 0.00 0.00 41.19 2.24
27 28 7.680730 ACACATTTTTCCAGAGTATGAGTACT 58.319 34.615 0.00 0.00 43.76 2.73
28 29 7.907214 ACACATTTTTCCAGAGTATGAGTAC 57.093 36.000 0.00 0.00 0.00 2.73
29 30 8.783093 CAAACACATTTTTCCAGAGTATGAGTA 58.217 33.333 0.00 0.00 0.00 2.59
30 31 7.255590 CCAAACACATTTTTCCAGAGTATGAGT 60.256 37.037 0.00 0.00 0.00 3.41
31 32 7.040478 TCCAAACACATTTTTCCAGAGTATGAG 60.040 37.037 0.00 0.00 0.00 2.90
32 33 6.775142 TCCAAACACATTTTTCCAGAGTATGA 59.225 34.615 0.00 0.00 0.00 2.15
33 34 6.980593 TCCAAACACATTTTTCCAGAGTATG 58.019 36.000 0.00 0.00 0.00 2.39
34 35 7.595819 TTCCAAACACATTTTTCCAGAGTAT 57.404 32.000 0.00 0.00 0.00 2.12
35 36 7.411486 TTTCCAAACACATTTTTCCAGAGTA 57.589 32.000 0.00 0.00 0.00 2.59
36 37 5.930837 TTCCAAACACATTTTTCCAGAGT 57.069 34.783 0.00 0.00 0.00 3.24
37 38 8.885494 TTATTTCCAAACACATTTTTCCAGAG 57.115 30.769 0.00 0.00 0.00 3.35
38 39 9.672673 TTTTATTTCCAAACACATTTTTCCAGA 57.327 25.926 0.00 0.00 0.00 3.86
39 40 9.934190 CTTTTATTTCCAAACACATTTTTCCAG 57.066 29.630 0.00 0.00 0.00 3.86
40 41 9.454859 ACTTTTATTTCCAAACACATTTTTCCA 57.545 25.926 0.00 0.00 0.00 3.53
65 66 7.362142 GGGAACATTTTCATAGAAGTGAGGAAC 60.362 40.741 0.00 0.00 32.80 3.62
73 75 4.635765 TCGCTGGGAACATTTTCATAGAAG 59.364 41.667 0.00 0.00 41.51 2.85
74 76 4.584874 TCGCTGGGAACATTTTCATAGAA 58.415 39.130 0.00 0.00 41.51 2.10
90 92 3.546002 TGGTTTATTCGTTTTCGCTGG 57.454 42.857 0.00 0.00 43.73 4.85
137 139 1.895020 ATTCGGCCGGTCAACTAGCA 61.895 55.000 27.83 0.00 0.00 3.49
146 148 1.856802 GTAATAACGATTCGGCCGGT 58.143 50.000 27.83 15.14 0.00 5.28
160 162 2.303163 ACCTGTCATTGCGCGTAATA 57.697 45.000 21.99 6.41 0.00 0.98
162 164 1.231221 AAACCTGTCATTGCGCGTAA 58.769 45.000 13.11 13.11 0.00 3.18
165 167 0.515127 TGTAAACCTGTCATTGCGCG 59.485 50.000 0.00 0.00 0.00 6.86
178 180 7.070322 TGGATAGGGAGGTACTAACATGTAAAC 59.930 40.741 0.00 0.00 41.55 2.01
179 181 7.134162 TGGATAGGGAGGTACTAACATGTAAA 58.866 38.462 0.00 0.00 41.55 2.01
180 182 6.685541 TGGATAGGGAGGTACTAACATGTAA 58.314 40.000 0.00 0.00 41.55 2.41
182 184 5.152306 TGGATAGGGAGGTACTAACATGT 57.848 43.478 0.00 0.00 41.55 3.21
188 190 4.422592 AGGTCAATGGATAGGGAGGTACTA 59.577 45.833 0.00 0.00 41.55 1.82
190 192 3.588569 AGGTCAATGGATAGGGAGGTAC 58.411 50.000 0.00 0.00 0.00 3.34
206 208 4.343814 TGATCCTATTTGACGCATAGGTCA 59.656 41.667 6.87 7.27 42.85 4.02
266 268 4.442375 TTTTCAGAAAAGGCGTCAACAA 57.558 36.364 4.06 0.00 0.00 2.83
277 279 9.677567 CGTTCAGGATTTATCTTTTTCAGAAAA 57.322 29.630 4.06 4.06 34.16 2.29
281 283 7.750903 GGAACGTTCAGGATTTATCTTTTTCAG 59.249 37.037 28.24 0.00 0.00 3.02
303 305 1.071699 TGCTATGGGCCTAATCGGAAC 59.928 52.381 4.53 0.00 40.92 3.62
305 307 1.429930 TTGCTATGGGCCTAATCGGA 58.570 50.000 4.53 0.00 40.92 4.55
307 309 2.416547 CGATTTGCTATGGGCCTAATCG 59.583 50.000 4.53 11.56 46.75 3.34
311 313 2.224523 CCTTCGATTTGCTATGGGCCTA 60.225 50.000 4.53 0.00 40.92 3.93
312 314 1.477558 CCTTCGATTTGCTATGGGCCT 60.478 52.381 4.53 0.00 40.92 5.19
313 315 0.954452 CCTTCGATTTGCTATGGGCC 59.046 55.000 0.00 0.00 40.92 5.80
354 356 2.821969 GTTGAACCTGTCATCCTTGCAT 59.178 45.455 0.00 0.00 35.70 3.96
358 360 6.681729 TTACTAGTTGAACCTGTCATCCTT 57.318 37.500 0.00 0.00 35.70 3.36
367 369 3.610911 GCCATGCTTACTAGTTGAACCT 58.389 45.455 0.00 0.00 0.00 3.50
372 374 4.882671 AATTCGCCATGCTTACTAGTTG 57.117 40.909 0.00 0.00 0.00 3.16
375 377 4.260784 GGACAAATTCGCCATGCTTACTAG 60.261 45.833 0.00 0.00 0.00 2.57
435 445 8.789881 TTTTATGACAATTTTAGTTGACACGG 57.210 30.769 0.00 0.00 36.79 4.94
600 636 4.783155 TTCCAAGGGAAGGGACCA 57.217 55.556 0.00 0.00 36.71 4.02
616 652 1.531423 CTGATGCCTCTGTTGTGCTT 58.469 50.000 0.00 0.00 0.00 3.91
618 654 1.930908 GCCTGATGCCTCTGTTGTGC 61.931 60.000 0.00 0.00 0.00 4.57
620 656 0.330604 ATGCCTGATGCCTCTGTTGT 59.669 50.000 0.00 0.00 40.16 3.32
621 657 0.738975 CATGCCTGATGCCTCTGTTG 59.261 55.000 0.00 0.00 40.16 3.33
622 658 0.622136 TCATGCCTGATGCCTCTGTT 59.378 50.000 0.00 0.00 40.16 3.16
623 659 0.180642 CTCATGCCTGATGCCTCTGT 59.819 55.000 0.00 0.00 40.16 3.41
624 660 0.468648 TCTCATGCCTGATGCCTCTG 59.531 55.000 0.00 0.00 40.16 3.35
625 661 0.469070 GTCTCATGCCTGATGCCTCT 59.531 55.000 0.00 0.00 40.16 3.69
626 662 0.879400 CGTCTCATGCCTGATGCCTC 60.879 60.000 0.00 0.00 40.16 4.70
627 663 1.145598 CGTCTCATGCCTGATGCCT 59.854 57.895 0.00 0.00 40.16 4.75
628 664 2.541120 GCGTCTCATGCCTGATGCC 61.541 63.158 13.01 1.30 38.77 4.40
629 665 1.523258 AGCGTCTCATGCCTGATGC 60.523 57.895 15.01 15.01 43.34 3.91
630 666 1.158484 CCAGCGTCTCATGCCTGATG 61.158 60.000 0.00 0.00 0.00 3.07
631 667 1.145598 CCAGCGTCTCATGCCTGAT 59.854 57.895 0.00 0.00 0.00 2.90
632 668 2.580815 CCAGCGTCTCATGCCTGA 59.419 61.111 0.00 0.00 0.00 3.86
633 669 2.513204 CCCAGCGTCTCATGCCTG 60.513 66.667 0.00 0.00 0.00 4.85
634 670 2.527951 GAACCCAGCGTCTCATGCCT 62.528 60.000 0.00 0.00 0.00 4.75
635 671 2.045926 AACCCAGCGTCTCATGCC 60.046 61.111 0.00 0.00 0.00 4.40
636 672 2.456119 CGAACCCAGCGTCTCATGC 61.456 63.158 0.00 0.00 0.00 4.06
637 673 1.079819 ACGAACCCAGCGTCTCATG 60.080 57.895 0.00 0.00 37.42 3.07
638 674 1.079819 CACGAACCCAGCGTCTCAT 60.080 57.895 0.00 0.00 40.44 2.90
639 675 2.338620 CACGAACCCAGCGTCTCA 59.661 61.111 0.00 0.00 40.44 3.27
640 676 2.432628 CCACGAACCCAGCGTCTC 60.433 66.667 0.00 0.00 40.44 3.36
641 677 4.681978 GCCACGAACCCAGCGTCT 62.682 66.667 0.00 0.00 40.44 4.18
662 698 4.456253 ACTCGGTGCGCTACGTCG 62.456 66.667 20.23 15.52 0.00 5.12
664 700 2.249557 CTACACTCGGTGCGCTACGT 62.250 60.000 20.23 0.00 36.98 3.57
666 702 0.522915 GACTACACTCGGTGCGCTAC 60.523 60.000 9.73 5.08 36.98 3.58
667 703 0.675837 AGACTACACTCGGTGCGCTA 60.676 55.000 9.73 0.00 36.98 4.26
668 704 0.675837 TAGACTACACTCGGTGCGCT 60.676 55.000 9.73 0.00 36.98 5.92
669 705 0.248134 CTAGACTACACTCGGTGCGC 60.248 60.000 0.00 0.00 36.98 6.09
670 706 1.085091 ACTAGACTACACTCGGTGCG 58.915 55.000 0.00 0.00 36.98 5.34
673 737 5.656416 ACTAGACTACTAGACTACACTCGGT 59.344 44.000 10.60 0.00 46.34 4.69
690 754 1.505353 GCGGTGCGTACACTAGACT 59.495 57.895 5.86 0.00 46.57 3.24
691 755 1.515736 GGCGGTGCGTACACTAGAC 60.516 63.158 5.86 0.00 46.57 2.59
692 756 2.879907 GGCGGTGCGTACACTAGA 59.120 61.111 5.86 0.00 46.57 2.43
694 758 4.781959 GCGGCGGTGCGTACACTA 62.782 66.667 9.78 0.00 46.57 2.74
710 774 0.249741 ATACTTATCGCCACCGGTGC 60.250 55.000 29.75 22.03 32.51 5.01
741 819 2.332362 GAATCACGCCATGCAGCTGG 62.332 60.000 17.12 1.68 39.45 4.85
742 820 1.063649 GAATCACGCCATGCAGCTG 59.936 57.895 10.11 10.11 0.00 4.24
743 821 2.117156 GGAATCACGCCATGCAGCT 61.117 57.895 0.00 0.00 0.00 4.24
744 822 1.936436 TTGGAATCACGCCATGCAGC 61.936 55.000 0.00 0.00 34.90 5.25
745 823 0.527113 TTTGGAATCACGCCATGCAG 59.473 50.000 0.00 0.00 34.90 4.41
746 824 0.964700 TTTTGGAATCACGCCATGCA 59.035 45.000 0.00 0.00 34.90 3.96
747 825 1.336702 TGTTTTGGAATCACGCCATGC 60.337 47.619 0.00 0.00 34.90 4.06
748 826 2.721274 TGTTTTGGAATCACGCCATG 57.279 45.000 0.00 0.00 34.90 3.66
749 827 5.398603 TTTATGTTTTGGAATCACGCCAT 57.601 34.783 0.00 0.00 34.90 4.40
750 828 4.855715 TTTATGTTTTGGAATCACGCCA 57.144 36.364 0.00 0.00 0.00 5.69
751 829 4.566360 CCATTTATGTTTTGGAATCACGCC 59.434 41.667 0.00 0.00 31.94 5.68
976 1054 1.079336 CTGCTGCTGCTACTCTGCA 60.079 57.895 17.00 0.00 45.55 4.41
1065 1155 1.800713 GTCGTCGAAGTCGGCCTTC 60.801 63.158 0.00 0.00 45.17 3.46
1194 1284 1.972588 AGAGGTACTTGGCCTTGGAT 58.027 50.000 3.32 0.00 41.55 3.41
1266 1356 2.079158 CGTACGTAGAAGGAGGTGACA 58.921 52.381 7.22 0.00 0.00 3.58
1288 1383 9.404348 GATGAAAGTGAAAAGAAGAAAAGGATC 57.596 33.333 0.00 0.00 0.00 3.36
1294 1398 7.519008 GCTCGAGATGAAAGTGAAAAGAAGAAA 60.519 37.037 18.75 0.00 0.00 2.52
1301 1405 4.212004 CACAGCTCGAGATGAAAGTGAAAA 59.788 41.667 35.32 0.00 35.09 2.29
1304 1408 2.928301 GCACAGCTCGAGATGAAAGTGA 60.928 50.000 35.32 0.00 35.09 3.41
1306 1410 1.274728 AGCACAGCTCGAGATGAAAGT 59.725 47.619 35.32 11.79 30.62 2.66
1307 1411 1.659601 CAGCACAGCTCGAGATGAAAG 59.340 52.381 35.32 23.62 36.40 2.62
1308 1412 1.673923 CCAGCACAGCTCGAGATGAAA 60.674 52.381 35.32 0.00 36.40 2.69
1309 1413 0.108472 CCAGCACAGCTCGAGATGAA 60.108 55.000 35.32 0.00 36.40 2.57
1310 1414 0.967380 TCCAGCACAGCTCGAGATGA 60.967 55.000 35.32 10.60 36.40 2.92
1311 1415 0.104487 ATCCAGCACAGCTCGAGATG 59.896 55.000 28.08 28.08 36.40 2.90
1312 1416 0.388659 GATCCAGCACAGCTCGAGAT 59.611 55.000 18.75 7.13 36.40 2.75
1313 1417 0.682532 AGATCCAGCACAGCTCGAGA 60.683 55.000 18.75 0.00 36.40 4.04
1316 1420 2.522836 AATAGATCCAGCACAGCTCG 57.477 50.000 0.00 0.00 36.40 5.03
1318 1422 3.641434 ACAAATAGATCCAGCACAGCT 57.359 42.857 0.00 0.00 40.77 4.24
1322 1426 4.775236 AGGAGAACAAATAGATCCAGCAC 58.225 43.478 0.00 0.00 32.21 4.40
1334 1438 8.865090 TCCATTTTATTTAGCAAGGAGAACAAA 58.135 29.630 0.00 0.00 0.00 2.83
1335 1439 8.415950 TCCATTTTATTTAGCAAGGAGAACAA 57.584 30.769 0.00 0.00 0.00 2.83
1337 1441 9.705290 TTTTCCATTTTATTTAGCAAGGAGAAC 57.295 29.630 0.00 0.00 0.00 3.01
1375 1486 0.178998 GGTCAGCTGCATCCATCCAT 60.179 55.000 9.47 0.00 0.00 3.41
1376 1487 1.225426 GGTCAGCTGCATCCATCCA 59.775 57.895 9.47 0.00 0.00 3.41
1377 1488 0.534652 GAGGTCAGCTGCATCCATCC 60.535 60.000 9.47 2.76 0.00 3.51
1379 1490 1.530771 GGAGGTCAGCTGCATCCAT 59.469 57.895 26.33 12.47 0.00 3.41
1380 1491 2.993008 GGAGGTCAGCTGCATCCA 59.007 61.111 26.33 2.81 0.00 3.41
1381 1492 2.202987 CGGAGGTCAGCTGCATCC 60.203 66.667 23.38 23.38 0.00 3.51
2294 3211 2.401583 ACGCATCCATACAAAGCTCA 57.598 45.000 0.00 0.00 0.00 4.26
2647 5017 5.257082 TCTCATCAATCACATGCAAATGG 57.743 39.130 0.00 0.00 0.00 3.16
2650 5032 6.376018 TCTTCATCTCATCAATCACATGCAAA 59.624 34.615 0.00 0.00 0.00 3.68
2711 5244 0.323957 GAACTAGCCCGGTCCACTTT 59.676 55.000 0.00 0.00 0.00 2.66
2714 5247 2.183555 CGAACTAGCCCGGTCCAC 59.816 66.667 0.00 0.00 0.00 4.02
2715 5248 3.766691 GCGAACTAGCCCGGTCCA 61.767 66.667 0.00 0.00 0.00 4.02
2716 5249 4.867599 CGCGAACTAGCCCGGTCC 62.868 72.222 0.00 0.00 0.00 4.46
2719 5252 4.867599 GGACGCGAACTAGCCCGG 62.868 72.222 15.93 0.00 0.00 5.73
2720 5253 1.793134 ATAGGACGCGAACTAGCCCG 61.793 60.000 15.93 0.00 0.00 6.13
2721 5254 0.318784 CATAGGACGCGAACTAGCCC 60.319 60.000 15.93 1.73 0.00 5.19
2722 5255 0.384669 ACATAGGACGCGAACTAGCC 59.615 55.000 15.93 3.85 0.00 3.93
2723 5256 1.478137 CACATAGGACGCGAACTAGC 58.522 55.000 15.93 0.00 0.00 3.42
2724 5257 1.404391 ACCACATAGGACGCGAACTAG 59.596 52.381 15.93 10.60 41.22 2.57
2727 5260 0.108992 TCACCACATAGGACGCGAAC 60.109 55.000 15.93 4.59 41.22 3.95
2736 5269 2.936993 GCCTGGTCTGTTCACCACATAG 60.937 54.545 0.00 0.00 41.84 2.23
2783 5330 3.389925 TCGTACCGAGACCAAAATGTT 57.610 42.857 0.00 0.00 0.00 2.71
2871 5577 1.136305 GATCACTGATCGGACGGGAAA 59.864 52.381 9.00 0.00 29.12 3.13
2874 5580 1.364171 GGATCACTGATCGGACGGG 59.636 63.158 9.00 0.00 39.72 5.28
2875 5581 1.008424 CGGATCACTGATCGGACGG 60.008 63.158 17.66 0.00 40.34 4.79
2879 5585 0.741326 AGTGTCGGATCACTGATCGG 59.259 55.000 16.80 16.80 45.40 4.18
2880 5586 2.098280 AGAAGTGTCGGATCACTGATCG 59.902 50.000 12.06 8.26 46.25 3.69
2882 5588 2.828520 ACAGAAGTGTCGGATCACTGAT 59.171 45.455 11.98 0.00 46.25 2.90
2883 5589 2.239400 ACAGAAGTGTCGGATCACTGA 58.761 47.619 11.98 0.00 46.25 3.41
2886 5592 3.728268 CGTCTACAGAAGTGTCGGATCAC 60.728 52.174 0.00 3.50 38.19 3.06


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

AutoCloner maintained by Alex Coulton.