Multiple sequence alignment - TraesCS4D01G355600

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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 TraesCS4D01G355600 chr4D 100.000 2879 0 0 1 2879 504596403 504599281 0.000000e+00 5317
1 TraesCS4D01G355600 chr5A 93.284 1638 66 17 750 2367 689251620 689253233 0.000000e+00 2375
2 TraesCS4D01G355600 chr5A 92.176 524 32 5 2357 2879 689253383 689253898 0.000000e+00 732
3 TraesCS4D01G355600 chr4B 92.179 1432 57 22 600 2012 651514030 651515425 0.000000e+00 1973
4 TraesCS4D01G355600 chr4B 91.929 793 35 14 2107 2877 651515434 651516219 0.000000e+00 1083
5 TraesCS4D01G355600 chr6D 88.023 860 93 9 983 1837 41207020 41207874 0.000000e+00 1009
6 TraesCS4D01G355600 chr6A 90.026 772 77 0 1066 1837 51760755 51761526 0.000000e+00 1000
7 TraesCS4D01G355600 chr6A 81.395 559 85 15 3 557 594244 594787 3.410000e-119 438
8 TraesCS4D01G355600 chr6B 87.850 856 96 7 986 1837 96655287 96654436 0.000000e+00 998
9 TraesCS4D01G355600 chr4A 86.842 836 106 4 997 1828 603666137 603666972 0.000000e+00 931
10 TraesCS4D01G355600 chr7B 86.358 843 109 6 997 1834 1437016 1437857 0.000000e+00 915
11 TraesCS4D01G355600 chr7B 88.336 763 87 2 1066 1827 1482356 1483117 0.000000e+00 915
12 TraesCS4D01G355600 chr7B 81.603 549 91 7 3 545 707963680 707963136 2.040000e-121 446
13 TraesCS4D01G355600 chr5D 87.742 775 95 0 1061 1835 556273506 556272732 0.000000e+00 905
14 TraesCS4D01G355600 chr5D 80.978 552 97 5 3 550 481520068 481520615 5.700000e-117 431
15 TraesCS4D01G355600 chr1D 82.169 544 84 10 9 547 224573253 224573788 3.380000e-124 455
16 TraesCS4D01G355600 chr1D 81.365 542 89 10 3 539 335039194 335039728 5.700000e-117 431
17 TraesCS4D01G355600 chr7D 82.103 542 85 9 11 547 636717228 636717762 1.220000e-123 453
18 TraesCS4D01G355600 chr7A 81.919 542 86 9 9 545 17635457 17634923 5.660000e-122 448
19 TraesCS4D01G355600 chr3B 81.455 550 90 9 3 546 753267907 753267364 9.470000e-120 440
20 TraesCS4D01G355600 chr2B 81.170 547 96 4 3 545 787078027 787077484 1.580000e-117 433


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 TraesCS4D01G355600 chr4D 504596403 504599281 2878 False 5317.0 5317 100.000 1 2879 1 chr4D.!!$F1 2878
1 TraesCS4D01G355600 chr5A 689251620 689253898 2278 False 1553.5 2375 92.730 750 2879 2 chr5A.!!$F1 2129
2 TraesCS4D01G355600 chr4B 651514030 651516219 2189 False 1528.0 1973 92.054 600 2877 2 chr4B.!!$F1 2277
3 TraesCS4D01G355600 chr6D 41207020 41207874 854 False 1009.0 1009 88.023 983 1837 1 chr6D.!!$F1 854
4 TraesCS4D01G355600 chr6A 51760755 51761526 771 False 1000.0 1000 90.026 1066 1837 1 chr6A.!!$F2 771
5 TraesCS4D01G355600 chr6A 594244 594787 543 False 438.0 438 81.395 3 557 1 chr6A.!!$F1 554
6 TraesCS4D01G355600 chr6B 96654436 96655287 851 True 998.0 998 87.850 986 1837 1 chr6B.!!$R1 851
7 TraesCS4D01G355600 chr4A 603666137 603666972 835 False 931.0 931 86.842 997 1828 1 chr4A.!!$F1 831
8 TraesCS4D01G355600 chr7B 1437016 1437857 841 False 915.0 915 86.358 997 1834 1 chr7B.!!$F1 837
9 TraesCS4D01G355600 chr7B 1482356 1483117 761 False 915.0 915 88.336 1066 1827 1 chr7B.!!$F2 761
10 TraesCS4D01G355600 chr7B 707963136 707963680 544 True 446.0 446 81.603 3 545 1 chr7B.!!$R1 542
11 TraesCS4D01G355600 chr5D 556272732 556273506 774 True 905.0 905 87.742 1061 1835 1 chr5D.!!$R1 774
12 TraesCS4D01G355600 chr5D 481520068 481520615 547 False 431.0 431 80.978 3 550 1 chr5D.!!$F1 547
13 TraesCS4D01G355600 chr1D 224573253 224573788 535 False 455.0 455 82.169 9 547 1 chr1D.!!$F1 538
14 TraesCS4D01G355600 chr1D 335039194 335039728 534 False 431.0 431 81.365 3 539 1 chr1D.!!$F2 536
15 TraesCS4D01G355600 chr7D 636717228 636717762 534 False 453.0 453 82.103 11 547 1 chr7D.!!$F1 536
16 TraesCS4D01G355600 chr7A 17634923 17635457 534 True 448.0 448 81.919 9 545 1 chr7A.!!$R1 536
17 TraesCS4D01G355600 chr3B 753267364 753267907 543 True 440.0 440 81.455 3 546 1 chr3B.!!$R1 543
18 TraesCS4D01G355600 chr2B 787077484 787078027 543 True 433.0 433 81.170 3 545 1 chr2B.!!$R1 542

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
336 352 0.036388 TTTCCTTCGGTGGCTGCTAG 60.036 55.0 0.0 0.0 0.0 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2013 0.901124 ACAGCCACAGACTGGAGATC 59.099 55.0 7.51 0.0 43.95 2.75 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
49 50 1.043673 GGTAGTCCAGGAGCGGATGT 61.044 60.000 0.00 0.00 37.41 3.06
58 60 3.149981 CAGGAGCGGATGTAGATAGTGA 58.850 50.000 0.00 0.00 0.00 3.41
60 62 4.944317 CAGGAGCGGATGTAGATAGTGATA 59.056 45.833 0.00 0.00 0.00 2.15
94 105 2.432628 GGAAGACGGCTCGTGTGG 60.433 66.667 0.00 0.00 41.37 4.17
113 124 2.596338 GGGTTCGTGGTTGGTGGG 60.596 66.667 0.00 0.00 0.00 4.61
116 127 1.153127 GTTCGTGGTTGGTGGGTGA 60.153 57.895 0.00 0.00 0.00 4.02
119 130 1.228124 CGTGGTTGGTGGGTGACAT 60.228 57.895 0.00 0.00 0.00 3.06
139 150 1.201424 GTATGGTTTCCTCCTCCGGT 58.799 55.000 0.00 0.00 0.00 5.28
143 154 0.399075 GGTTTCCTCCTCCGGTTTCA 59.601 55.000 0.00 0.00 0.00 2.69
152 164 1.278238 CTCCGGTTTCATAGTCGTGC 58.722 55.000 0.00 0.00 0.00 5.34
160 172 3.075005 ATAGTCGTGCGGGGTGCT 61.075 61.111 0.00 0.00 46.63 4.40
165 177 2.186903 CGTGCGGGGTGCTAGATT 59.813 61.111 0.00 0.00 46.63 2.40
171 183 0.815615 CGGGGTGCTAGATTTGGAGC 60.816 60.000 0.00 0.00 39.25 4.70
189 201 1.292223 CTTGATGACGTGTCCGGGT 59.708 57.895 0.00 0.00 38.78 5.28
209 221 1.299976 GTTGCCCCGGTCTGATTCT 59.700 57.895 0.00 0.00 0.00 2.40
215 227 2.945890 GCCCCGGTCTGATTCTTTCAAT 60.946 50.000 0.00 0.00 32.78 2.57
223 235 5.803967 GGTCTGATTCTTTCAATGACAATGC 59.196 40.000 0.00 0.00 33.36 3.56
228 240 5.787953 TTCTTTCAATGACAATGCCTTCA 57.212 34.783 0.00 0.00 0.00 3.02
240 255 2.957402 TGCCTTCATCTTTGGTGAGT 57.043 45.000 0.00 0.00 0.00 3.41
276 291 3.604875 CAAAGCTGCATTTCAGGGATT 57.395 42.857 1.02 0.00 43.06 3.01
298 313 2.761195 CCACGTCGAGCTCGGATGA 61.761 63.158 33.98 13.87 40.29 2.92
336 352 0.036388 TTTCCTTCGGTGGCTGCTAG 60.036 55.000 0.00 0.00 0.00 3.42
342 358 3.009115 GGTGGCTGCTAGGGTGGA 61.009 66.667 0.00 0.00 0.00 4.02
350 366 0.840288 TGCTAGGGTGGAGCCAAAGA 60.840 55.000 0.00 0.00 39.30 2.52
351 367 0.107459 GCTAGGGTGGAGCCAAAGAG 60.107 60.000 0.00 0.00 39.65 2.85
353 369 1.909302 CTAGGGTGGAGCCAAAGAGAA 59.091 52.381 0.00 0.00 39.65 2.87
386 402 2.373169 TGGTGTCAAGCTCAGAGGATTT 59.627 45.455 0.00 0.00 0.00 2.17
389 405 4.320788 GGTGTCAAGCTCAGAGGATTTTTG 60.321 45.833 0.00 0.00 0.00 2.44
391 407 4.074970 GTCAAGCTCAGAGGATTTTTGGA 58.925 43.478 0.00 0.00 0.00 3.53
419 435 8.816640 TTGATTGTAATTTTTCTTCTTGGCTC 57.183 30.769 0.00 0.00 0.00 4.70
436 452 1.597937 GCTCGTGTTCCTTTGTGCAAG 60.598 52.381 0.00 0.00 0.00 4.01
455 471 3.283259 AGGGCTAGTATTTTGCTGTCC 57.717 47.619 0.00 0.00 0.00 4.02
465 481 6.507023 AGTATTTTGCTGTCCTTTCAGTTTG 58.493 36.000 0.00 0.00 37.70 2.93
466 482 4.799564 TTTTGCTGTCCTTTCAGTTTGT 57.200 36.364 0.00 0.00 37.70 2.83
469 485 3.620488 TGCTGTCCTTTCAGTTTGTTCT 58.380 40.909 0.00 0.00 37.70 3.01
470 486 4.016444 TGCTGTCCTTTCAGTTTGTTCTT 58.984 39.130 0.00 0.00 37.70 2.52
475 491 5.125417 TGTCCTTTCAGTTTGTTCTTCTTGG 59.875 40.000 0.00 0.00 0.00 3.61
476 492 5.125578 GTCCTTTCAGTTTGTTCTTCTTGGT 59.874 40.000 0.00 0.00 0.00 3.67
477 493 5.714806 TCCTTTCAGTTTGTTCTTCTTGGTT 59.285 36.000 0.00 0.00 0.00 3.67
480 496 5.309323 TCAGTTTGTTCTTCTTGGTTGTG 57.691 39.130 0.00 0.00 0.00 3.33
482 498 5.242838 TCAGTTTGTTCTTCTTGGTTGTGTT 59.757 36.000 0.00 0.00 0.00 3.32
499 515 6.255453 GGTTGTGTTTACGTGACTTGTACTAA 59.745 38.462 0.00 0.00 0.00 2.24
504 520 7.806960 GTGTTTACGTGACTTGTACTAAGATCT 59.193 37.037 0.00 0.00 0.00 2.75
539 556 4.413520 AGGAGACATGTATTACCCTGCAAT 59.586 41.667 0.00 0.00 0.00 3.56
542 559 6.942576 GGAGACATGTATTACCCTGCAATAAT 59.057 38.462 0.00 0.00 0.00 1.28
579 596 7.462571 AATATAGGTGTTGGTCTTTGTTTCC 57.537 36.000 0.00 0.00 0.00 3.13
580 597 3.094484 AGGTGTTGGTCTTTGTTTCCA 57.906 42.857 0.00 0.00 0.00 3.53
581 598 3.642141 AGGTGTTGGTCTTTGTTTCCAT 58.358 40.909 0.00 0.00 0.00 3.41
582 599 3.384467 AGGTGTTGGTCTTTGTTTCCATG 59.616 43.478 0.00 0.00 0.00 3.66
583 600 3.383185 GGTGTTGGTCTTTGTTTCCATGA 59.617 43.478 0.00 0.00 0.00 3.07
584 601 4.359706 GTGTTGGTCTTTGTTTCCATGAC 58.640 43.478 0.00 0.00 0.00 3.06
585 602 3.383185 TGTTGGTCTTTGTTTCCATGACC 59.617 43.478 0.00 0.00 41.30 4.02
586 603 3.593442 TGGTCTTTGTTTCCATGACCT 57.407 42.857 11.07 0.00 41.39 3.85
587 604 4.715534 TGGTCTTTGTTTCCATGACCTA 57.284 40.909 11.07 0.00 41.39 3.08
588 605 4.651778 TGGTCTTTGTTTCCATGACCTAG 58.348 43.478 11.07 0.00 41.39 3.02
589 606 4.010349 GGTCTTTGTTTCCATGACCTAGG 58.990 47.826 7.41 7.41 39.50 3.02
590 607 4.506802 GGTCTTTGTTTCCATGACCTAGGT 60.507 45.833 16.26 16.26 39.50 3.08
591 608 4.695928 GTCTTTGTTTCCATGACCTAGGTC 59.304 45.833 31.61 31.61 44.77 3.85
609 626 8.450434 ACCTAGGTCAAAATTAAAAGAAGGGTA 58.550 33.333 9.21 0.00 0.00 3.69
631 648 9.747293 GGGTATATCTTAGGCGTCTTATATTTC 57.253 37.037 0.00 0.00 0.00 2.17
641 658 4.700700 CGTCTTATATTTCGGAAAGGGGT 58.299 43.478 9.30 0.00 0.00 4.95
649 666 3.343941 TTCGGAAAGGGGTGAGTATTG 57.656 47.619 0.00 0.00 0.00 1.90
650 667 1.065709 TCGGAAAGGGGTGAGTATTGC 60.066 52.381 0.00 0.00 0.00 3.56
651 668 1.379527 GGAAAGGGGTGAGTATTGCG 58.620 55.000 0.00 0.00 0.00 4.85
652 669 1.379527 GAAAGGGGTGAGTATTGCGG 58.620 55.000 0.00 0.00 0.00 5.69
653 670 0.679960 AAAGGGGTGAGTATTGCGGC 60.680 55.000 0.00 0.00 0.00 6.53
654 671 2.516225 GGGGTGAGTATTGCGGCC 60.516 66.667 0.00 0.00 0.00 6.13
655 672 2.270850 GGGTGAGTATTGCGGCCA 59.729 61.111 2.24 0.00 0.00 5.36
674 692 3.493129 GCCAAAATTTGAAAAGGTCCGAC 59.507 43.478 7.37 0.00 0.00 4.79
727 745 6.107343 GGTGAACTTGAGGGAGTAGAATTAC 58.893 44.000 0.00 0.00 0.00 1.89
819 837 9.774742 CTTGTAATTTGTAAATAGTGCTTCCTC 57.225 33.333 0.00 0.00 0.00 3.71
820 838 7.970384 TGTAATTTGTAAATAGTGCTTCCTCG 58.030 34.615 0.00 0.00 0.00 4.63
880 900 1.341187 TGCATGCTCAATGATGGTGGA 60.341 47.619 20.33 0.00 38.72 4.02
881 901 1.961394 GCATGCTCAATGATGGTGGAT 59.039 47.619 11.37 0.00 38.72 3.41
882 902 2.364324 GCATGCTCAATGATGGTGGATT 59.636 45.455 11.37 0.00 38.72 3.01
883 903 3.798889 GCATGCTCAATGATGGTGGATTG 60.799 47.826 11.37 0.00 38.72 2.67
884 904 2.380941 TGCTCAATGATGGTGGATTGG 58.619 47.619 0.00 0.00 31.59 3.16
885 905 2.291735 TGCTCAATGATGGTGGATTGGT 60.292 45.455 0.00 0.00 31.59 3.67
886 906 2.100252 GCTCAATGATGGTGGATTGGTG 59.900 50.000 0.00 0.00 31.59 4.17
887 907 2.691526 CTCAATGATGGTGGATTGGTGG 59.308 50.000 0.00 0.00 31.59 4.61
912 932 7.158021 GCCTTCCTCTATATATATGGATGCAC 58.842 42.308 9.03 12.12 0.00 4.57
945 981 3.738982 TGGACACAACACTTCATAGGTG 58.261 45.455 0.00 0.00 40.19 4.00
956 992 8.571336 CAACACTTCATAGGTGAAATTTTCTCT 58.429 33.333 10.33 9.77 43.39 3.10
973 1009 3.875571 TCTCTCCCTTCTTTTCTTCCCT 58.124 45.455 0.00 0.00 0.00 4.20
980 1016 6.858941 TCCCTTCTTTTCTTCCCTAATTCAA 58.141 36.000 0.00 0.00 0.00 2.69
1290 1337 2.969238 GGCATGATCGCCGTCCTG 60.969 66.667 0.00 0.00 43.52 3.86
1898 1945 2.100631 CCAGCACCATCGTTCGTCC 61.101 63.158 0.00 0.00 0.00 4.79
1951 2013 9.952188 CAGATCCACATATATTACGTACTATGG 57.048 37.037 13.95 9.09 0.00 2.74
1952 2014 9.916360 AGATCCACATATATTACGTACTATGGA 57.084 33.333 13.95 13.24 36.96 3.41
1955 2017 9.916360 TCCACATATATTACGTACTATGGATCT 57.084 33.333 13.95 0.00 0.00 2.75
2051 2114 2.702592 TCGTTGAGTTTTCACCACCT 57.297 45.000 0.00 0.00 31.71 4.00
2058 2121 6.565999 CGTTGAGTTTTCACCACCTTATCTTC 60.566 42.308 0.00 0.00 31.71 2.87
2061 2124 6.710744 TGAGTTTTCACCACCTTATCTTCTTC 59.289 38.462 0.00 0.00 0.00 2.87
2066 2129 2.912956 ACCACCTTATCTTCTTCTGCCA 59.087 45.455 0.00 0.00 0.00 4.92
2067 2130 3.330701 ACCACCTTATCTTCTTCTGCCAA 59.669 43.478 0.00 0.00 0.00 4.52
2068 2131 3.944015 CCACCTTATCTTCTTCTGCCAAG 59.056 47.826 0.00 0.00 0.00 3.61
2069 2132 4.566488 CCACCTTATCTTCTTCTGCCAAGT 60.566 45.833 0.00 0.00 0.00 3.16
2070 2133 5.006386 CACCTTATCTTCTTCTGCCAAGTT 58.994 41.667 0.00 0.00 0.00 2.66
2073 2136 5.295540 CCTTATCTTCTTCTGCCAAGTTAGC 59.704 44.000 0.00 0.00 0.00 3.09
2077 2140 4.528596 TCTTCTTCTGCCAAGTTAGCTAGT 59.471 41.667 0.00 0.00 0.00 2.57
2080 2143 6.354794 TCTTCTGCCAAGTTAGCTAGTTAA 57.645 37.500 0.00 0.00 0.00 2.01
2102 2165 1.597742 ACTGCAAAATGAGTGACGCT 58.402 45.000 0.00 0.00 0.00 5.07
2103 2166 1.265095 ACTGCAAAATGAGTGACGCTG 59.735 47.619 0.00 0.00 0.00 5.18
2104 2167 0.040157 TGCAAAATGAGTGACGCTGC 60.040 50.000 0.00 0.00 0.00 5.25
2105 2168 0.040157 GCAAAATGAGTGACGCTGCA 60.040 50.000 0.00 0.00 0.00 4.41
2149 2212 4.124351 CCGTAGTTCTCGCCGGCA 62.124 66.667 28.98 12.94 33.20 5.69
2150 2213 2.126228 CGTAGTTCTCGCCGGCAA 60.126 61.111 28.98 7.25 0.00 4.52
2153 2216 1.373748 TAGTTCTCGCCGGCAACAC 60.374 57.895 28.98 16.66 0.00 3.32
2286 2357 4.367450 ACACATGTGTTGCCAATGTAAAC 58.633 39.130 25.76 0.00 41.83 2.01
2307 2390 9.180678 GTAAACCATAAAGATTCACAACAACAG 57.819 33.333 0.00 0.00 0.00 3.16
2317 2400 4.185467 TCACAACAACAGCAACAAACAT 57.815 36.364 0.00 0.00 0.00 2.71
2374 2617 7.611855 AGACAATGTAAGGGAGGAATTACAAAG 59.388 37.037 2.28 1.66 43.14 2.77
2494 2737 2.533318 CTGCAAGTCGGTCCTTCAC 58.467 57.895 0.00 0.00 0.00 3.18
2518 2761 5.512788 CAGACAATGACAAAACATATTCGGC 59.487 40.000 0.00 0.00 0.00 5.54
2545 2788 4.770010 TTGATCCACAATTTCTGGGTAACC 59.230 41.667 0.00 0.00 45.73 2.85
2577 2820 3.792956 GCACAAAATCCATTAGCACATCG 59.207 43.478 0.00 0.00 0.00 3.84
2711 2954 2.245096 GCGCAACTGCTGTAAATTCAG 58.755 47.619 0.30 0.00 39.32 3.02
2788 3032 9.736023 AAAACACTCTTAGAACTAGCAAAATTG 57.264 29.630 0.00 0.00 0.00 2.32
2819 3064 3.667360 TCCGTTTTAGAACTTAGGGCAC 58.333 45.455 0.00 0.00 33.51 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 5.642063 TGTCGTCGATGCATATCACTATCTA 59.358 40.000 0.00 0.00 32.67 1.98
58 60 2.558359 TCCAGATGTCGTCGATGCATAT 59.442 45.455 0.00 8.36 0.00 1.78
60 62 0.746659 TCCAGATGTCGTCGATGCAT 59.253 50.000 0.00 0.00 0.00 3.96
83 85 4.619227 AACCCACCACACGAGCCG 62.619 66.667 0.00 0.00 0.00 5.52
86 88 1.954146 CACGAACCCACCACACGAG 60.954 63.158 0.00 0.00 0.00 4.18
94 105 2.190841 CCACCAACCACGAACCCAC 61.191 63.158 0.00 0.00 0.00 4.61
113 124 4.192317 GAGGAGGAAACCATACATGTCAC 58.808 47.826 0.00 0.00 0.00 3.67
116 127 2.170607 CGGAGGAGGAAACCATACATGT 59.829 50.000 2.69 2.69 0.00 3.21
139 150 0.390603 CACCCCGCACGACTATGAAA 60.391 55.000 0.00 0.00 0.00 2.69
143 154 1.735376 CTAGCACCCCGCACGACTAT 61.735 60.000 0.00 0.00 46.13 2.12
152 164 0.815615 GCTCCAAATCTAGCACCCCG 60.816 60.000 0.00 0.00 38.63 5.73
160 172 4.183865 CACGTCATCAAGCTCCAAATCTA 58.816 43.478 0.00 0.00 0.00 1.98
165 177 1.608025 GGACACGTCATCAAGCTCCAA 60.608 52.381 0.00 0.00 0.00 3.53
171 183 0.320421 AACCCGGACACGTCATCAAG 60.320 55.000 0.73 0.00 38.78 3.02
189 201 0.608035 GAATCAGACCGGGGCAACAA 60.608 55.000 6.32 0.00 39.74 2.83
209 221 5.988310 AGATGAAGGCATTGTCATTGAAA 57.012 34.783 0.00 0.00 34.61 2.69
215 227 3.256383 CACCAAAGATGAAGGCATTGTCA 59.744 43.478 0.00 0.00 34.11 3.58
253 268 0.038892 CCTGAAATGCAGCTTTGCGT 60.039 50.000 0.00 0.00 43.50 5.24
267 282 0.036388 GACGTGGCTCAATCCCTGAA 60.036 55.000 0.00 0.00 32.17 3.02
272 287 2.167861 GCTCGACGTGGCTCAATCC 61.168 63.158 0.00 0.00 0.00 3.01
295 310 2.094100 ATGACGGATCACCTCCTCAT 57.906 50.000 0.00 0.00 42.47 2.90
298 313 3.721087 AAAAATGACGGATCACCTCCT 57.279 42.857 0.00 0.00 42.47 3.69
336 352 0.402121 ACTTCTCTTTGGCTCCACCC 59.598 55.000 0.00 0.00 37.83 4.61
342 358 1.615384 GCCCATCACTTCTCTTTGGCT 60.615 52.381 0.00 0.00 34.83 4.75
350 366 1.076024 ACACCAATGCCCATCACTTCT 59.924 47.619 0.00 0.00 0.00 2.85
351 367 1.474077 GACACCAATGCCCATCACTTC 59.526 52.381 0.00 0.00 0.00 3.01
353 369 0.405198 TGACACCAATGCCCATCACT 59.595 50.000 0.00 0.00 0.00 3.41
386 402 9.541143 GAAGAAAAATTACAATCAAGGTCCAAA 57.459 29.630 0.00 0.00 0.00 3.28
389 405 9.196552 CAAGAAGAAAAATTACAATCAAGGTCC 57.803 33.333 0.00 0.00 0.00 4.46
391 407 7.657354 GCCAAGAAGAAAAATTACAATCAAGGT 59.343 33.333 0.00 0.00 0.00 3.50
408 424 1.048601 AGGAACACGAGCCAAGAAGA 58.951 50.000 0.00 0.00 0.00 2.87
436 452 3.283259 AGGACAGCAAAATACTAGCCC 57.717 47.619 0.00 0.00 0.00 5.19
443 459 6.463995 ACAAACTGAAAGGACAGCAAAATA 57.536 33.333 0.00 0.00 41.06 1.40
455 471 6.308766 CACAACCAAGAAGAACAAACTGAAAG 59.691 38.462 0.00 0.00 42.29 2.62
465 481 5.025826 CACGTAAACACAACCAAGAAGAAC 58.974 41.667 0.00 0.00 0.00 3.01
466 482 4.936411 TCACGTAAACACAACCAAGAAGAA 59.064 37.500 0.00 0.00 0.00 2.52
469 485 4.255301 AGTCACGTAAACACAACCAAGAA 58.745 39.130 0.00 0.00 0.00 2.52
470 486 3.864243 AGTCACGTAAACACAACCAAGA 58.136 40.909 0.00 0.00 0.00 3.02
475 491 5.707411 AGTACAAGTCACGTAAACACAAC 57.293 39.130 0.00 0.00 0.00 3.32
476 492 7.257003 TCTTAGTACAAGTCACGTAAACACAA 58.743 34.615 0.00 0.00 0.00 3.33
477 493 6.794374 TCTTAGTACAAGTCACGTAAACACA 58.206 36.000 0.00 0.00 0.00 3.72
480 496 8.739649 AAGATCTTAGTACAAGTCACGTAAAC 57.260 34.615 6.06 0.00 0.00 2.01
514 530 4.966168 TGCAGGGTAATACATGTCTCCTTA 59.034 41.667 0.00 0.00 0.00 2.69
553 570 9.185680 GGAAACAAAGACCAACACCTATATTAT 57.814 33.333 0.00 0.00 0.00 1.28
554 571 8.164733 TGGAAACAAAGACCAACACCTATATTA 58.835 33.333 0.00 0.00 37.44 0.98
555 572 7.007723 TGGAAACAAAGACCAACACCTATATT 58.992 34.615 0.00 0.00 37.44 1.28
556 573 6.548321 TGGAAACAAAGACCAACACCTATAT 58.452 36.000 0.00 0.00 37.44 0.86
557 574 5.942961 TGGAAACAAAGACCAACACCTATA 58.057 37.500 0.00 0.00 37.44 1.31
558 575 4.798882 TGGAAACAAAGACCAACACCTAT 58.201 39.130 0.00 0.00 37.44 2.57
559 576 4.237976 TGGAAACAAAGACCAACACCTA 57.762 40.909 0.00 0.00 37.44 3.08
560 577 3.094484 TGGAAACAAAGACCAACACCT 57.906 42.857 0.00 0.00 37.44 4.00
568 585 4.695928 GACCTAGGTCATGGAAACAAAGAC 59.304 45.833 32.91 3.78 44.22 3.01
569 586 4.906618 GACCTAGGTCATGGAAACAAAGA 58.093 43.478 32.91 0.00 44.02 2.52
582 599 7.450634 ACCCTTCTTTTAATTTTGACCTAGGTC 59.549 37.037 31.61 31.61 44.77 3.85
583 600 7.302948 ACCCTTCTTTTAATTTTGACCTAGGT 58.697 34.615 16.26 16.26 0.00 3.08
584 601 7.776618 ACCCTTCTTTTAATTTTGACCTAGG 57.223 36.000 7.41 7.41 0.00 3.02
594 611 9.503399 CGCCTAAGATATACCCTTCTTTTAATT 57.497 33.333 0.00 0.00 34.22 1.40
595 612 8.657712 ACGCCTAAGATATACCCTTCTTTTAAT 58.342 33.333 0.00 0.00 34.22 1.40
596 613 8.026396 ACGCCTAAGATATACCCTTCTTTTAA 57.974 34.615 0.00 0.00 34.22 1.52
597 614 7.508296 AGACGCCTAAGATATACCCTTCTTTTA 59.492 37.037 0.00 0.00 34.22 1.52
598 615 6.326843 AGACGCCTAAGATATACCCTTCTTTT 59.673 38.462 0.00 0.00 34.22 2.27
609 626 8.289939 TCCGAAATATAAGACGCCTAAGATAT 57.710 34.615 0.00 0.00 0.00 1.63
612 629 6.395426 TTCCGAAATATAAGACGCCTAAGA 57.605 37.500 0.00 0.00 0.00 2.10
617 634 3.497262 CCCTTTCCGAAATATAAGACGCC 59.503 47.826 0.00 0.00 0.00 5.68
618 635 3.497262 CCCCTTTCCGAAATATAAGACGC 59.503 47.826 0.00 0.00 0.00 5.19
631 648 1.379527 GCAATACTCACCCCTTTCCG 58.620 55.000 0.00 0.00 0.00 4.30
641 658 3.256879 TCAAATTTTGGCCGCAATACTCA 59.743 39.130 9.18 0.00 0.00 3.41
649 666 2.217750 ACCTTTTCAAATTTTGGCCGC 58.782 42.857 9.18 0.00 0.00 6.53
650 667 2.805671 GGACCTTTTCAAATTTTGGCCG 59.194 45.455 9.18 0.00 0.00 6.13
651 668 2.805671 CGGACCTTTTCAAATTTTGGCC 59.194 45.455 9.18 0.00 0.00 5.36
652 669 3.493129 GTCGGACCTTTTCAAATTTTGGC 59.507 43.478 9.18 0.00 0.00 4.52
653 670 4.744631 CAGTCGGACCTTTTCAAATTTTGG 59.255 41.667 9.18 0.00 0.00 3.28
654 671 5.587289 TCAGTCGGACCTTTTCAAATTTTG 58.413 37.500 4.14 2.59 0.00 2.44
655 672 5.845391 TCAGTCGGACCTTTTCAAATTTT 57.155 34.783 4.14 0.00 0.00 1.82
694 712 6.043938 ACTCCCTCAAGTTCACCAATAACTTA 59.956 38.462 1.24 0.00 43.52 2.24
727 745 8.506437 TGTTTTGCATTCAAGATTCAGTAGTAG 58.494 33.333 0.00 0.00 33.12 2.57
734 752 8.991026 CCTTTTATGTTTTGCATTCAAGATTCA 58.009 29.630 0.00 0.00 38.94 2.57
735 753 7.959109 GCCTTTTATGTTTTGCATTCAAGATTC 59.041 33.333 0.00 0.00 38.94 2.52
736 754 7.444792 TGCCTTTTATGTTTTGCATTCAAGATT 59.555 29.630 0.00 0.00 38.94 2.40
747 765 4.756135 ACAAGCCATGCCTTTTATGTTTTG 59.244 37.500 0.00 0.00 0.00 2.44
828 848 2.557920 AGCCAAGCCTATGCATACTC 57.442 50.000 1.16 0.00 41.13 2.59
840 860 1.418908 TATGCCTCCCCTAGCCAAGC 61.419 60.000 0.00 0.00 0.00 4.01
841 861 1.004044 CATATGCCTCCCCTAGCCAAG 59.996 57.143 0.00 0.00 0.00 3.61
842 862 1.067295 CATATGCCTCCCCTAGCCAA 58.933 55.000 0.00 0.00 0.00 4.52
844 864 1.301293 GCATATGCCTCCCCTAGCC 59.699 63.158 17.26 0.00 34.31 3.93
880 900 7.072961 CCATATATATAGAGGAAGGCCACCAAT 59.927 40.741 18.84 12.05 36.29 3.16
881 901 6.386927 CCATATATATAGAGGAAGGCCACCAA 59.613 42.308 18.84 6.50 36.29 3.67
882 902 5.905331 CCATATATATAGAGGAAGGCCACCA 59.095 44.000 18.84 1.60 36.29 4.17
883 903 6.143915 TCCATATATATAGAGGAAGGCCACC 58.856 44.000 5.01 8.40 36.29 4.61
884 904 7.675062 CATCCATATATATAGAGGAAGGCCAC 58.325 42.308 16.45 0.00 36.29 5.01
885 905 6.270927 GCATCCATATATATAGAGGAAGGCCA 59.729 42.308 20.02 0.00 36.29 5.36
886 906 6.270927 TGCATCCATATATATAGAGGAAGGCC 59.729 42.308 23.52 0.00 34.06 5.19
887 907 7.158021 GTGCATCCATATATATAGAGGAAGGC 58.842 42.308 21.81 21.81 34.96 4.35
912 932 0.754957 TGTGTCCAACTTGGCCAAGG 60.755 55.000 41.04 28.56 42.53 3.61
941 963 5.590976 AGAAGGGAGAGAAAATTTCACCT 57.409 39.130 8.55 6.93 0.00 4.00
943 965 7.946207 AGAAAAGAAGGGAGAGAAAATTTCAC 58.054 34.615 8.55 1.59 0.00 3.18
945 981 8.085296 GGAAGAAAAGAAGGGAGAGAAAATTTC 58.915 37.037 0.00 0.00 0.00 2.17
956 992 6.463053 TGAATTAGGGAAGAAAAGAAGGGA 57.537 37.500 0.00 0.00 0.00 4.20
980 1016 6.511416 GCCATATCAATATCTATCGAGCTGT 58.489 40.000 0.00 0.00 0.00 4.40
1020 1061 1.874345 CGTTGGCCTCCGTACTCAGT 61.874 60.000 3.32 0.00 0.00 3.41
1290 1337 4.814294 CCGGCGGTGCAGTAGACC 62.814 72.222 19.97 0.00 0.00 3.85
1898 1945 4.090354 CCAACCAAGTACGTTACGTATGTG 59.910 45.833 20.52 18.92 44.12 3.21
1951 2013 0.901124 ACAGCCACAGACTGGAGATC 59.099 55.000 7.51 0.00 43.95 2.75
1952 2014 1.356124 AACAGCCACAGACTGGAGAT 58.644 50.000 7.51 0.00 43.95 2.75
1953 2015 1.895798 CTAACAGCCACAGACTGGAGA 59.104 52.381 7.51 0.00 43.95 3.71
1954 2016 1.620819 ACTAACAGCCACAGACTGGAG 59.379 52.381 7.51 0.00 43.95 3.86
1955 2017 1.717032 ACTAACAGCCACAGACTGGA 58.283 50.000 7.51 0.00 43.95 3.86
1956 2018 2.550830 AACTAACAGCCACAGACTGG 57.449 50.000 7.51 0.00 44.08 4.00
1957 2019 5.237815 TCATAAACTAACAGCCACAGACTG 58.762 41.667 0.00 0.00 41.08 3.51
1958 2020 5.483685 TCATAAACTAACAGCCACAGACT 57.516 39.130 0.00 0.00 0.00 3.24
1959 2021 6.743575 AATCATAAACTAACAGCCACAGAC 57.256 37.500 0.00 0.00 0.00 3.51
1960 2022 8.100791 AGTAAATCATAAACTAACAGCCACAGA 58.899 33.333 0.00 0.00 0.00 3.41
1961 2023 8.268850 AGTAAATCATAAACTAACAGCCACAG 57.731 34.615 0.00 0.00 0.00 3.66
1962 2024 9.899661 ATAGTAAATCATAAACTAACAGCCACA 57.100 29.630 0.00 0.00 30.03 4.17
2051 2114 6.054860 AGCTAACTTGGCAGAAGAAGATAA 57.945 37.500 0.00 0.00 0.00 1.75
2058 2121 7.617041 AATTAACTAGCTAACTTGGCAGAAG 57.383 36.000 0.00 0.00 0.00 2.85
2061 2124 7.466050 GCAGTAATTAACTAGCTAACTTGGCAG 60.466 40.741 0.00 0.00 35.76 4.85
2070 2133 9.667107 ACTCATTTTGCAGTAATTAACTAGCTA 57.333 29.630 0.00 0.00 35.76 3.32
2073 2136 9.760660 GTCACTCATTTTGCAGTAATTAACTAG 57.239 33.333 0.00 0.00 35.76 2.57
2077 2140 6.072728 AGCGTCACTCATTTTGCAGTAATTAA 60.073 34.615 0.00 0.00 0.00 1.40
2080 2143 3.753272 AGCGTCACTCATTTTGCAGTAAT 59.247 39.130 0.00 0.00 0.00 1.89
2102 2165 1.530720 CAAACGTACAGAGTGCATGCA 59.469 47.619 18.46 18.46 0.00 3.96
2103 2166 1.725931 GCAAACGTACAGAGTGCATGC 60.726 52.381 11.82 11.82 34.75 4.06
2104 2167 1.135972 GGCAAACGTACAGAGTGCATG 60.136 52.381 9.26 0.00 35.76 4.06
2105 2168 1.156736 GGCAAACGTACAGAGTGCAT 58.843 50.000 9.26 0.00 35.76 3.96
2148 2211 8.675705 TTGACCCATTCATATACATAGTGTTG 57.324 34.615 0.00 0.00 32.84 3.33
2149 2212 9.288576 CATTGACCCATTCATATACATAGTGTT 57.711 33.333 0.00 0.00 32.84 3.32
2150 2213 7.391554 GCATTGACCCATTCATATACATAGTGT 59.608 37.037 0.00 0.00 32.84 3.55
2153 2216 7.926674 TGCATTGACCCATTCATATACATAG 57.073 36.000 0.00 0.00 32.84 2.23
2286 2357 5.771469 TGCTGTTGTTGTGAATCTTTATGG 58.229 37.500 0.00 0.00 0.00 2.74
2307 2390 9.855021 AGTAGGAACAATAAATATGTTTGTTGC 57.145 29.630 19.52 15.82 45.08 4.17
2410 2653 3.117888 CAGTTATATGACAGGTGGCCCTT 60.118 47.826 0.00 0.00 39.89 3.95
2465 2708 1.192534 CGACTTGCAGTTTCGTTCCTC 59.807 52.381 5.73 0.00 0.00 3.71
2494 2737 5.512788 GCCGAATATGTTTTGTCATTGTCTG 59.487 40.000 0.00 0.00 0.00 3.51
2518 2761 3.367292 CCCAGAAATTGTGGATCAAACCG 60.367 47.826 11.06 0.00 39.62 4.44
2545 2788 1.606224 GGATTTTGTGCAGGGCAACAG 60.606 52.381 0.00 0.00 41.47 3.16
2577 2820 6.801862 GCTAGTCACACATTTTGTACATTTCC 59.198 38.462 0.00 0.00 35.67 3.13
2819 3064 6.478016 GCTTGTAATACCCGTTTTCTACTAGG 59.522 42.308 0.00 0.00 0.00 3.02
2826 3071 2.476686 GGCGCTTGTAATACCCGTTTTC 60.477 50.000 7.64 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.