Multiple sequence alignment - TraesCS3B01G479400

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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 TraesCS3B01G479400 chr3B 100.000 2975 0 0 1 2975 727465288 727462314 0.000000e+00 5494
1 TraesCS3B01G479400 chr3B 82.910 433 61 10 1553 1984 727422389 727421969 7.780000e-101 377
2 TraesCS3B01G479400 chr3B 79.707 478 82 12 2010 2482 228695892 228695425 6.150000e-87 331
3 TraesCS3B01G479400 chr3B 73.615 686 120 39 1279 1926 728199408 728200070 1.080000e-49 207
4 TraesCS3B01G479400 chr3D 87.181 2036 192 33 9 2011 548675835 548673836 0.000000e+00 2250
5 TraesCS3B01G479400 chr3D 84.190 1031 99 33 1005 1984 548635668 548634651 0.000000e+00 942
6 TraesCS3B01G479400 chr3D 82.836 938 132 24 2030 2947 609252827 609251899 0.000000e+00 813
7 TraesCS3B01G479400 chr3A 84.172 2028 234 41 1 1984 686163898 686161914 0.000000e+00 1886
8 TraesCS3B01G479400 chr3A 84.277 1024 103 27 1005 1984 686158220 686157211 0.000000e+00 946
9 TraesCS3B01G479400 chr3A 84.842 442 60 6 2023 2459 742860435 742859996 3.520000e-119 438
10 TraesCS3B01G479400 chr5B 89.026 975 87 16 2011 2975 263781492 263782456 0.000000e+00 1190
11 TraesCS3B01G479400 chr5D 88.568 971 91 17 2011 2975 197856281 197855325 0.000000e+00 1160
12 TraesCS3B01G479400 chr5D 84.679 966 99 22 2030 2975 495474634 495475570 0.000000e+00 918
13 TraesCS3B01G479400 chr7D 82.341 974 122 30 2035 2975 18877165 18876209 0.000000e+00 800
14 TraesCS3B01G479400 chr7D 85.435 666 74 16 2325 2975 469201931 469202588 0.000000e+00 671
15 TraesCS3B01G479400 chr4A 83.850 774 101 18 2026 2782 713123225 713123991 0.000000e+00 715
16 TraesCS3B01G479400 chr7B 82.512 812 113 20 2028 2819 113048418 113047616 0.000000e+00 686
17 TraesCS3B01G479400 chr7B 84.226 672 74 25 2323 2975 492749373 492750031 2.520000e-175 625


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 TraesCS3B01G479400 chr3B 727462314 727465288 2974 True 5494 5494 100.0000 1 2975 1 chr3B.!!$R3 2974
1 TraesCS3B01G479400 chr3B 728199408 728200070 662 False 207 207 73.6150 1279 1926 1 chr3B.!!$F1 647
2 TraesCS3B01G479400 chr3D 548673836 548675835 1999 True 2250 2250 87.1810 9 2011 1 chr3D.!!$R2 2002
3 TraesCS3B01G479400 chr3D 548634651 548635668 1017 True 942 942 84.1900 1005 1984 1 chr3D.!!$R1 979
4 TraesCS3B01G479400 chr3D 609251899 609252827 928 True 813 813 82.8360 2030 2947 1 chr3D.!!$R3 917
5 TraesCS3B01G479400 chr3A 686157211 686163898 6687 True 1416 1886 84.2245 1 1984 2 chr3A.!!$R2 1983
6 TraesCS3B01G479400 chr5B 263781492 263782456 964 False 1190 1190 89.0260 2011 2975 1 chr5B.!!$F1 964
7 TraesCS3B01G479400 chr5D 197855325 197856281 956 True 1160 1160 88.5680 2011 2975 1 chr5D.!!$R1 964
8 TraesCS3B01G479400 chr5D 495474634 495475570 936 False 918 918 84.6790 2030 2975 1 chr5D.!!$F1 945
9 TraesCS3B01G479400 chr7D 18876209 18877165 956 True 800 800 82.3410 2035 2975 1 chr7D.!!$R1 940
10 TraesCS3B01G479400 chr7D 469201931 469202588 657 False 671 671 85.4350 2325 2975 1 chr7D.!!$F1 650
11 TraesCS3B01G479400 chr4A 713123225 713123991 766 False 715 715 83.8500 2026 2782 1 chr4A.!!$F1 756
12 TraesCS3B01G479400 chr7B 113047616 113048418 802 True 686 686 82.5120 2028 2819 1 chr7B.!!$R1 791
13 TraesCS3B01G479400 chr7B 492749373 492750031 658 False 625 625 84.2260 2323 2975 1 chr7B.!!$F1 652

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
234 240 0.036388 ATGGCTCTCGCGGAAAAAGA 60.036 50.0 6.13 0.00 36.88 2.52 F
424 440 0.110328 AGTACGCGTTGAGTCAGTCG 60.110 55.0 20.78 13.09 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1660 0.622154 AGAGGAGGACGAGGAGGAGA 60.622 60.000 0.0 0.00 0.00 3.71 R
2019 2138 1.326245 GTTGCAACGCACGAGCATATA 59.674 47.619 14.9 0.15 38.71 0.86 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
36 37 5.590259 TCCAAGATAGAAGCACAATTTAGCC 59.410 40.000 0.00 0.00 0.00 3.93
70 71 1.860641 TTCGAGAGGCATTGTCCCTA 58.139 50.000 0.00 0.00 31.41 3.53
76 77 3.205815 GGCATTGTCCCTATGGCAA 57.794 52.632 0.00 0.00 45.09 4.52
77 78 1.484038 GGCATTGTCCCTATGGCAAA 58.516 50.000 0.00 0.00 45.09 3.68
90 91 5.395546 CCCTATGGCAAAAGCAAATATGTGT 60.396 40.000 0.00 0.00 0.00 3.72
92 93 4.870123 TGGCAAAAGCAAATATGTGTCT 57.130 36.364 0.00 0.00 0.00 3.41
94 95 5.229423 TGGCAAAAGCAAATATGTGTCTTC 58.771 37.500 0.00 0.00 0.00 2.87
98 99 1.062587 AGCAAATATGTGTCTTCGCGC 59.937 47.619 0.00 0.00 0.00 6.86
101 102 1.200483 AATATGTGTCTTCGCGCGAG 58.800 50.000 32.74 24.86 0.00 5.03
103 104 1.929806 TATGTGTCTTCGCGCGAGGT 61.930 55.000 35.78 21.79 0.00 3.85
108 109 0.997196 GTCTTCGCGCGAGGTAAATT 59.003 50.000 35.78 0.00 0.00 1.82
112 113 0.733566 TCGCGCGAGGTAAATTCGTT 60.734 50.000 31.40 0.00 40.08 3.85
166 167 4.799715 TTCCCTTTTCCTTGAGGTACAA 57.200 40.909 0.00 0.00 36.97 2.41
188 189 3.067106 CTGTGCCTCACGTAGAAACAAT 58.933 45.455 0.00 0.00 37.14 2.71
192 193 4.927425 GTGCCTCACGTAGAAACAATCTTA 59.073 41.667 0.00 0.00 39.71 2.10
199 200 5.812642 CACGTAGAAACAATCTTATGCCTCT 59.187 40.000 0.00 0.00 39.71 3.69
200 201 5.812642 ACGTAGAAACAATCTTATGCCTCTG 59.187 40.000 0.00 0.00 39.71 3.35
201 202 5.812642 CGTAGAAACAATCTTATGCCTCTGT 59.187 40.000 0.00 0.00 39.71 3.41
204 205 5.645497 AGAAACAATCTTATGCCTCTGTGAC 59.355 40.000 0.00 0.00 33.39 3.67
213 214 1.881973 TGCCTCTGTGACAAGCAAATC 59.118 47.619 2.58 0.00 0.00 2.17
218 219 2.821378 TCTGTGACAAGCAAATCCATGG 59.179 45.455 4.97 4.97 0.00 3.66
223 224 2.097825 ACAAGCAAATCCATGGCTCTC 58.902 47.619 6.96 0.00 36.76 3.20
226 232 1.645455 CAAATCCATGGCTCTCGCG 59.355 57.895 6.96 0.00 36.88 5.87
227 233 1.524621 AAATCCATGGCTCTCGCGG 60.525 57.895 6.96 0.00 36.88 6.46
233 239 0.097674 CATGGCTCTCGCGGAAAAAG 59.902 55.000 6.13 0.00 36.88 2.27
234 240 0.036388 ATGGCTCTCGCGGAAAAAGA 60.036 50.000 6.13 0.00 36.88 2.52
236 242 1.362406 GGCTCTCGCGGAAAAAGAGG 61.362 60.000 19.60 5.69 37.58 3.69
238 244 1.939838 GCTCTCGCGGAAAAAGAGGAA 60.940 52.381 19.60 0.00 37.58 3.36
239 245 2.413837 CTCTCGCGGAAAAAGAGGAAA 58.586 47.619 6.13 0.00 34.24 3.13
240 246 3.003480 CTCTCGCGGAAAAAGAGGAAAT 58.997 45.455 6.13 0.00 34.24 2.17
241 247 2.742053 TCTCGCGGAAAAAGAGGAAATG 59.258 45.455 6.13 0.00 33.16 2.32
242 248 2.484264 CTCGCGGAAAAAGAGGAAATGT 59.516 45.455 6.13 0.00 0.00 2.71
243 249 3.666274 TCGCGGAAAAAGAGGAAATGTA 58.334 40.909 6.13 0.00 0.00 2.29
244 250 4.258543 TCGCGGAAAAAGAGGAAATGTAT 58.741 39.130 6.13 0.00 0.00 2.29
245 251 4.698304 TCGCGGAAAAAGAGGAAATGTATT 59.302 37.500 6.13 0.00 0.00 1.89
246 252 5.182380 TCGCGGAAAAAGAGGAAATGTATTT 59.818 36.000 6.13 0.00 0.00 1.40
247 253 5.861787 CGCGGAAAAAGAGGAAATGTATTTT 59.138 36.000 0.00 0.00 0.00 1.82
248 254 6.364976 CGCGGAAAAAGAGGAAATGTATTTTT 59.635 34.615 0.00 0.00 36.17 1.94
293 301 5.509716 TCTACCTCTCGCGAATGAAAATA 57.490 39.130 11.33 0.00 0.00 1.40
299 307 3.871006 TCTCGCGAATGAAAATATGTGCT 59.129 39.130 11.33 0.00 0.00 4.40
322 330 3.896888 TCCACAAAGGAGCAAATCAATGT 59.103 39.130 0.00 0.00 43.07 2.71
327 335 5.048224 ACAAAGGAGCAAATCAATGTCTCTG 60.048 40.000 0.00 0.00 0.00 3.35
377 393 0.546122 AGGCAGAACTGTTGTCCACA 59.454 50.000 0.00 0.00 0.00 4.17
379 395 1.378531 GCAGAACTGTTGTCCACACA 58.621 50.000 0.00 0.00 0.00 3.72
380 396 1.064060 GCAGAACTGTTGTCCACACAC 59.936 52.381 0.00 0.00 29.76 3.82
391 407 3.239449 TGTCCACACACTGTTCTCCTAT 58.761 45.455 0.00 0.00 0.00 2.57
404 420 1.971505 CTCCTATGCGCCAAGGGTGA 61.972 60.000 21.23 5.35 34.74 4.02
409 425 0.676782 ATGCGCCAAGGGTGAAGTAC 60.677 55.000 4.18 0.00 34.74 2.73
411 427 2.388232 CGCCAAGGGTGAAGTACGC 61.388 63.158 0.00 0.00 42.19 4.42
424 440 0.110328 AGTACGCGTTGAGTCAGTCG 60.110 55.000 20.78 13.09 0.00 4.18
431 447 1.021390 GTTGAGTCAGTCGGGCATGG 61.021 60.000 0.00 0.00 0.00 3.66
436 452 0.535335 GTCAGTCGGGCATGGAGTTA 59.465 55.000 0.00 0.00 0.00 2.24
443 459 2.026729 TCGGGCATGGAGTTATGTTCAA 60.027 45.455 0.00 0.00 0.00 2.69
444 460 2.097466 CGGGCATGGAGTTATGTTCAAC 59.903 50.000 0.00 0.00 0.00 3.18
448 464 4.220602 GGCATGGAGTTATGTTCAACCTTT 59.779 41.667 0.00 0.00 0.00 3.11
452 468 4.753107 TGGAGTTATGTTCAACCTTTCGAC 59.247 41.667 0.00 0.00 0.00 4.20
493 509 1.903404 CGGCCTTGGCCTCTGTTTT 60.903 57.895 25.99 0.00 0.00 2.43
494 510 1.463553 CGGCCTTGGCCTCTGTTTTT 61.464 55.000 25.99 0.00 0.00 1.94
497 513 1.000171 GCCTTGGCCTCTGTTTTTCTG 60.000 52.381 3.32 0.00 0.00 3.02
505 521 3.551659 GCCTCTGTTTTTCTGCCTCTTTG 60.552 47.826 0.00 0.00 0.00 2.77
515 531 0.874390 TGCCTCTTTGTCATTCGTGC 59.126 50.000 0.00 0.00 0.00 5.34
524 540 0.716108 GTCATTCGTGCCTTGAGACG 59.284 55.000 0.00 0.00 36.91 4.18
525 541 0.601057 TCATTCGTGCCTTGAGACGA 59.399 50.000 0.00 0.00 42.61 4.20
527 543 2.895039 TTCGTGCCTTGAGACGAAC 58.105 52.632 0.00 0.00 46.63 3.95
530 546 0.934496 CGTGCCTTGAGACGAACAAA 59.066 50.000 0.00 0.00 37.81 2.83
549 567 5.254901 ACAAAGGGTTGTGTGTAGTTGTAA 58.745 37.500 0.00 0.00 46.40 2.41
555 573 5.703592 GGGTTGTGTGTAGTTGTAATCATGA 59.296 40.000 0.00 0.00 0.00 3.07
569 587 2.655090 TCATGATGGGTGTGTTGTGT 57.345 45.000 0.00 0.00 0.00 3.72
571 589 2.158696 TCATGATGGGTGTGTTGTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
628 648 4.814234 AGATGTGTCTAGATCTGAGTCGAC 59.186 45.833 7.70 7.70 35.76 4.20
632 652 4.632251 GTGTCTAGATCTGAGTCGACTGAA 59.368 45.833 25.58 10.18 0.00 3.02
636 656 4.695217 AGATCTGAGTCGACTGAAACTC 57.305 45.455 25.58 11.07 41.84 3.01
637 657 4.331968 AGATCTGAGTCGACTGAAACTCT 58.668 43.478 25.58 13.18 41.97 3.24
638 658 4.764823 AGATCTGAGTCGACTGAAACTCTT 59.235 41.667 25.58 0.00 41.97 2.85
639 659 5.941058 AGATCTGAGTCGACTGAAACTCTTA 59.059 40.000 25.58 0.43 41.97 2.10
640 660 5.614923 TCTGAGTCGACTGAAACTCTTAG 57.385 43.478 25.58 2.58 41.97 2.18
646 675 4.383351 GTCGACTGAAACTCTTAGTCAAGC 59.617 45.833 8.70 0.00 40.57 4.01
657 686 3.740832 TCTTAGTCAAGCGACACAACATG 59.259 43.478 0.00 0.00 45.23 3.21
670 699 6.858993 GCGACACAACATGTAAAAAGGAATAA 59.141 34.615 0.00 0.00 43.56 1.40
704 734 9.846248 AATAAACTTTTATGCACAGATCTTCAC 57.154 29.630 0.00 0.00 33.85 3.18
705 735 5.536554 ACTTTTATGCACAGATCTTCACG 57.463 39.130 0.00 0.00 0.00 4.35
710 740 2.337583 TGCACAGATCTTCACGTAAGC 58.662 47.619 0.00 0.00 45.62 3.09
719 749 4.316205 TCTTCACGTAAGCTCTCACAAA 57.684 40.909 0.00 0.00 45.62 2.83
721 751 4.686091 TCTTCACGTAAGCTCTCACAAATG 59.314 41.667 0.00 0.00 45.62 2.32
729 759 5.536554 AAGCTCTCACAAATGTAACATCG 57.463 39.130 0.00 0.00 0.00 3.84
730 760 4.820897 AGCTCTCACAAATGTAACATCGA 58.179 39.130 0.00 0.00 0.00 3.59
731 761 4.627467 AGCTCTCACAAATGTAACATCGAC 59.373 41.667 0.00 0.00 0.00 4.20
732 762 4.201724 GCTCTCACAAATGTAACATCGACC 60.202 45.833 0.00 0.00 0.00 4.79
733 763 3.924073 TCTCACAAATGTAACATCGACCG 59.076 43.478 0.00 0.00 0.00 4.79
734 764 3.915536 TCACAAATGTAACATCGACCGA 58.084 40.909 0.00 0.00 0.00 4.69
735 765 3.924073 TCACAAATGTAACATCGACCGAG 59.076 43.478 0.00 0.00 0.00 4.63
756 786 3.192422 AGATGAAGTCTCGGTTGACTGAG 59.808 47.826 12.72 12.72 45.49 3.35
767 797 4.870426 TCGGTTGACTGAGATTTAGCAATC 59.130 41.667 0.00 0.00 39.45 2.67
768 798 4.631377 CGGTTGACTGAGATTTAGCAATCA 59.369 41.667 0.19 0.00 41.37 2.57
799 829 7.500141 AGAAAATTGTAAAGTGGCAAATCTGT 58.500 30.769 0.00 0.00 0.00 3.41
802 832 3.734463 TGTAAAGTGGCAAATCTGTCGA 58.266 40.909 0.00 0.00 0.00 4.20
803 833 4.130857 TGTAAAGTGGCAAATCTGTCGAA 58.869 39.130 0.00 0.00 0.00 3.71
854 885 1.269998 CTCCGAAAGTCCAAGTCGTCT 59.730 52.381 0.00 0.00 32.93 4.18
855 886 1.268899 TCCGAAAGTCCAAGTCGTCTC 59.731 52.381 0.00 0.00 32.93 3.36
901 932 0.673333 ACGACTGCGATGCAAATCCA 60.673 50.000 0.00 0.00 38.41 3.41
904 935 2.279741 GACTGCGATGCAAATCCACTA 58.720 47.619 0.00 0.00 38.41 2.74
907 938 3.065786 ACTGCGATGCAAATCCACTAATG 59.934 43.478 0.00 0.00 38.41 1.90
908 939 3.016031 TGCGATGCAAATCCACTAATGT 58.984 40.909 0.00 0.00 34.76 2.71
966 1006 0.387202 TCAAGCTCTCTCGCATAGCC 59.613 55.000 0.00 0.00 36.92 3.93
968 1008 0.388659 AAGCTCTCTCGCATAGCCAG 59.611 55.000 0.00 0.00 36.92 4.85
969 1009 0.754957 AGCTCTCTCGCATAGCCAGT 60.755 55.000 0.00 0.00 36.92 4.00
977 1017 1.417517 TCGCATAGCCAGTTGATCCAT 59.582 47.619 0.00 0.00 0.00 3.41
1038 1078 4.719369 AACGCAGGCTCGTCGTCC 62.719 66.667 11.35 0.00 42.46 4.79
1141 1181 2.584391 GCCCACACCTTCGTCTCCT 61.584 63.158 0.00 0.00 0.00 3.69
1167 1207 2.844839 GCCCTCCTCTACGCCCAT 60.845 66.667 0.00 0.00 0.00 4.00
1170 1210 1.152440 CCTCCTCTACGCCCATCCT 60.152 63.158 0.00 0.00 0.00 3.24
1222 1262 2.525629 TGGCCAGGGAGAACGACA 60.526 61.111 0.00 0.00 0.00 4.35
1223 1263 1.903877 CTGGCCAGGGAGAACGACAT 61.904 60.000 26.14 0.00 0.00 3.06
1237 1295 4.332268 AGAACGACATCTACGACTTCTACC 59.668 45.833 0.00 0.00 29.22 3.18
1511 1587 2.836154 GTCCTGGTGCTGGTGGAA 59.164 61.111 0.00 0.00 0.00 3.53
1584 1660 0.320771 CAGGCTACGTGCTGTTCCTT 60.321 55.000 0.00 0.00 42.39 3.36
1840 1958 4.719369 GCGGCGTCTTCGGTGTCT 62.719 66.667 9.37 0.00 37.56 3.41
1953 2071 7.734924 TTATTATGAATCTGTCATGCCACTC 57.265 36.000 0.00 0.00 46.85 3.51
1954 2072 2.014335 TGAATCTGTCATGCCACTCG 57.986 50.000 0.00 0.00 0.00 4.18
1971 2089 1.590238 CTCGCGATGAAACAAGCTAGG 59.410 52.381 10.36 0.00 0.00 3.02
1991 2110 8.710835 GCTAGGTAGCTAAATCCTTTATGATC 57.289 38.462 6.70 0.00 45.62 2.92
1996 2115 8.994170 GGTAGCTAAATCCTTTATGATCTGAAC 58.006 37.037 0.00 0.00 0.00 3.18
2005 2124 8.893219 TCCTTTATGATCTGAACATGTATGAC 57.107 34.615 10.31 0.00 0.00 3.06
2008 2127 8.437360 TTTATGATCTGAACATGTATGACACC 57.563 34.615 10.31 0.00 0.00 4.16
2019 2138 4.568072 TGTATGACACCCACTAGCAAAT 57.432 40.909 0.00 0.00 0.00 2.32
2074 2311 7.761038 AATAATACACCCTAGCCAAATAAGC 57.239 36.000 0.00 0.00 0.00 3.09
2169 2417 0.761187 CCCACCCTCATCGATGATGT 59.239 55.000 27.43 22.88 40.55 3.06
2203 2451 3.690628 ACATGATCACAATGCATTCGACA 59.309 39.130 9.53 10.12 0.00 4.35
2218 2466 1.979308 TCGACATGGTAAACCCCAAGA 59.021 47.619 0.00 0.00 38.20 3.02
2219 2467 2.372504 TCGACATGGTAAACCCCAAGAA 59.627 45.455 0.00 0.00 38.20 2.52
2241 2492 3.890936 GAGCTTCCCACTGCACGCT 62.891 63.158 0.00 0.00 0.00 5.07
2366 4499 9.090692 CAAAAACTAATCAAATCCAAGGCATAG 57.909 33.333 0.00 0.00 0.00 2.23
2395 4528 2.336554 TGAACGCCTACTACGAACAC 57.663 50.000 0.00 0.00 0.00 3.32
2609 5296 9.767684 TTCATGAATATGTTTTGAATACACGAC 57.232 29.630 3.38 0.00 35.73 4.34
2611 5298 7.915293 TGAATATGTTTTGAATACACGACCT 57.085 32.000 0.00 0.00 0.00 3.85
2651 5346 7.838696 TGAACATTATTGTATTCCCCAATCACT 59.161 33.333 0.00 0.00 34.06 3.41
2837 5592 2.553602 ACGAACATTTTACGGTTTCCCC 59.446 45.455 0.00 0.00 0.00 4.81
2839 5594 3.609879 CGAACATTTTACGGTTTCCCCAC 60.610 47.826 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.730215 TGGGGCTAAATTGTGCTTCTA 57.270 42.857 3.48 0.00 0.00 2.10
48 49 1.066143 GGGACAATGCCTCTCGAAAGA 60.066 52.381 0.00 0.00 39.12 2.52
62 63 2.300956 TGCTTTTGCCATAGGGACAA 57.699 45.000 0.00 0.00 46.87 3.18
70 71 5.410355 AGACACATATTTGCTTTTGCCAT 57.590 34.783 0.00 0.00 46.87 4.40
75 76 4.158384 CGCGAAGACACATATTTGCTTTT 58.842 39.130 0.00 0.00 34.73 2.27
76 77 3.747193 CGCGAAGACACATATTTGCTTT 58.253 40.909 0.00 0.00 34.73 3.51
77 78 2.476185 GCGCGAAGACACATATTTGCTT 60.476 45.455 12.10 0.00 34.73 3.91
90 91 1.274596 GAATTTACCTCGCGCGAAGA 58.725 50.000 33.10 18.65 0.00 2.87
92 93 0.733566 ACGAATTTACCTCGCGCGAA 60.734 50.000 33.99 19.27 39.97 4.70
94 95 0.314021 GAACGAATTTACCTCGCGCG 60.314 55.000 26.76 26.76 39.97 6.86
101 102 2.603560 CTGCGAGAGGAACGAATTTACC 59.396 50.000 0.00 0.00 0.00 2.85
103 104 3.861276 TCTGCGAGAGGAACGAATTTA 57.139 42.857 0.00 0.00 0.00 1.40
108 109 1.244816 TTCTTCTGCGAGAGGAACGA 58.755 50.000 6.62 0.00 35.72 3.85
142 143 5.520751 TGTACCTCAAGGAAAAGGGAAAAA 58.479 37.500 2.30 0.00 36.95 1.94
152 153 2.486548 GGCACAGTTGTACCTCAAGGAA 60.487 50.000 2.30 0.00 36.66 3.36
166 167 1.411246 TGTTTCTACGTGAGGCACAGT 59.589 47.619 0.00 0.00 33.40 3.55
177 178 5.812642 ACAGAGGCATAAGATTGTTTCTACG 59.187 40.000 0.00 0.00 33.05 3.51
188 189 2.302733 TGCTTGTCACAGAGGCATAAGA 59.697 45.455 0.00 0.00 0.00 2.10
192 193 1.985473 TTTGCTTGTCACAGAGGCAT 58.015 45.000 3.59 0.00 32.87 4.40
199 200 1.273048 GCCATGGATTTGCTTGTCACA 59.727 47.619 18.40 0.00 0.00 3.58
200 201 1.547372 AGCCATGGATTTGCTTGTCAC 59.453 47.619 18.40 0.00 29.17 3.67
201 202 1.820519 GAGCCATGGATTTGCTTGTCA 59.179 47.619 18.40 0.00 34.99 3.58
204 205 1.065102 CGAGAGCCATGGATTTGCTTG 59.935 52.381 18.40 2.64 34.99 4.01
223 224 2.989422 ACATTTCCTCTTTTTCCGCG 57.011 45.000 0.00 0.00 0.00 6.46
274 282 4.271049 CACATATTTTCATTCGCGAGAGGT 59.729 41.667 9.59 0.00 43.69 3.85
275 283 4.766007 CACATATTTTCATTCGCGAGAGG 58.234 43.478 9.59 2.88 43.69 3.69
293 301 1.251251 GCTCCTTTGTGGAAGCACAT 58.749 50.000 0.00 0.00 45.63 3.21
299 307 4.344679 ACATTGATTTGCTCCTTTGTGGAA 59.655 37.500 0.00 0.00 45.63 3.53
305 313 4.461781 CCAGAGACATTGATTTGCTCCTTT 59.538 41.667 0.00 0.00 0.00 3.11
309 317 2.223203 CGCCAGAGACATTGATTTGCTC 60.223 50.000 0.00 0.00 0.00 4.26
319 327 3.289797 TCTCTTCCGCCAGAGACAT 57.710 52.632 7.52 0.00 43.72 3.06
322 330 3.703001 AAAATTCTCTTCCGCCAGAGA 57.297 42.857 7.52 7.52 46.35 3.10
353 369 1.070758 GACAACAGTTCTGCCTCTCCA 59.929 52.381 0.00 0.00 0.00 3.86
363 379 2.356135 ACAGTGTGTGGACAACAGTTC 58.644 47.619 0.00 0.00 40.26 3.01
377 393 0.108138 GGCGCATAGGAGAACAGTGT 60.108 55.000 10.83 0.00 0.00 3.55
379 395 0.613260 TTGGCGCATAGGAGAACAGT 59.387 50.000 10.83 0.00 0.00 3.55
380 396 1.293924 CTTGGCGCATAGGAGAACAG 58.706 55.000 10.83 0.00 0.00 3.16
391 407 1.302192 GTACTTCACCCTTGGCGCA 60.302 57.895 10.83 0.00 0.00 6.09
404 420 1.662309 CGACTGACTCAACGCGTACTT 60.662 52.381 14.46 0.00 0.00 2.24
409 425 2.805353 CCCGACTGACTCAACGCG 60.805 66.667 3.53 3.53 0.00 6.01
411 427 1.079819 ATGCCCGACTGACTCAACG 60.080 57.895 0.00 0.00 0.00 4.10
424 440 2.427095 GGTTGAACATAACTCCATGCCC 59.573 50.000 0.00 0.00 0.00 5.36
431 447 4.446719 ACGTCGAAAGGTTGAACATAACTC 59.553 41.667 0.00 0.00 0.00 3.01
436 452 2.557317 ACACGTCGAAAGGTTGAACAT 58.443 42.857 0.00 0.00 0.00 2.71
443 459 2.012937 TGTTGAACACGTCGAAAGGT 57.987 45.000 0.00 0.00 0.00 3.50
444 460 3.001838 TCAATGTTGAACACGTCGAAAGG 59.998 43.478 0.00 0.00 33.55 3.11
448 464 3.804873 TCAATCAATGTTGAACACGTCGA 59.195 39.130 0.00 0.00 41.13 4.20
452 468 4.143835 CGTCTCAATCAATGTTGAACACG 58.856 43.478 0.00 0.00 41.13 4.49
491 507 3.882888 ACGAATGACAAAGAGGCAGAAAA 59.117 39.130 0.00 0.00 39.86 2.29
493 509 2.807967 CACGAATGACAAAGAGGCAGAA 59.192 45.455 0.00 0.00 39.86 3.02
494 510 2.416747 CACGAATGACAAAGAGGCAGA 58.583 47.619 0.00 0.00 39.86 4.26
497 513 0.169009 GGCACGAATGACAAAGAGGC 59.831 55.000 0.00 0.00 32.03 4.70
505 521 0.716108 CGTCTCAAGGCACGAATGAC 59.284 55.000 0.00 0.00 38.32 3.06
515 531 2.256117 ACCCTTTGTTCGTCTCAAGG 57.744 50.000 0.00 0.00 0.00 3.61
524 540 4.157105 ACAACTACACACAACCCTTTGTTC 59.843 41.667 0.00 0.00 43.89 3.18
525 541 4.083565 ACAACTACACACAACCCTTTGTT 58.916 39.130 0.00 0.00 43.89 2.83
527 543 5.821516 TTACAACTACACACAACCCTTTG 57.178 39.130 0.00 0.00 38.83 2.77
530 546 5.298989 TGATTACAACTACACACAACCCT 57.701 39.130 0.00 0.00 0.00 4.34
549 567 3.084039 GACACAACACACCCATCATGAT 58.916 45.455 1.18 1.18 0.00 2.45
555 573 2.703536 TCTAGTGACACAACACACCCAT 59.296 45.455 8.59 0.00 42.45 4.00
607 627 4.574421 CAGTCGACTCAGATCTAGACACAT 59.426 45.833 16.96 0.00 0.00 3.21
611 631 5.353123 AGTTTCAGTCGACTCAGATCTAGAC 59.647 44.000 16.96 4.67 0.00 2.59
612 632 5.492895 AGTTTCAGTCGACTCAGATCTAGA 58.507 41.667 16.96 4.35 0.00 2.43
616 636 4.695217 AGAGTTTCAGTCGACTCAGATC 57.305 45.455 16.96 10.33 43.65 2.75
621 641 5.359716 TGACTAAGAGTTTCAGTCGACTC 57.640 43.478 16.96 4.27 41.29 3.36
625 645 3.362237 CGCTTGACTAAGAGTTTCAGTCG 59.638 47.826 0.00 0.00 41.29 4.18
628 648 4.149046 GTGTCGCTTGACTAAGAGTTTCAG 59.851 45.833 0.00 0.00 43.29 3.02
632 652 3.728076 TGTGTCGCTTGACTAAGAGTT 57.272 42.857 0.00 0.00 43.29 3.01
636 656 3.494626 ACATGTTGTGTCGCTTGACTAAG 59.505 43.478 0.00 0.00 43.29 2.18
637 657 3.462982 ACATGTTGTGTCGCTTGACTAA 58.537 40.909 0.00 0.00 43.29 2.24
638 658 3.106242 ACATGTTGTGTCGCTTGACTA 57.894 42.857 0.00 0.00 43.29 2.59
639 659 1.953559 ACATGTTGTGTCGCTTGACT 58.046 45.000 0.00 0.00 43.29 3.41
640 660 3.870723 TTACATGTTGTGTCGCTTGAC 57.129 42.857 2.30 0.00 42.29 3.18
646 675 8.789881 TTTATTCCTTTTTACATGTTGTGTCG 57.210 30.769 2.30 0.00 42.29 4.35
679 708 8.177663 CGTGAAGATCTGTGCATAAAAGTTTAT 58.822 33.333 0.00 0.00 33.82 1.40
704 734 5.839262 TGTTACATTTGTGAGAGCTTACG 57.161 39.130 0.00 0.00 0.00 3.18
705 735 6.310467 TCGATGTTACATTTGTGAGAGCTTAC 59.690 38.462 0.00 0.00 0.00 2.34
710 740 4.031765 CGGTCGATGTTACATTTGTGAGAG 59.968 45.833 0.00 0.00 0.00 3.20
719 749 4.098044 ACTTCATCTCGGTCGATGTTACAT 59.902 41.667 0.00 0.00 41.17 2.29
721 751 4.030134 ACTTCATCTCGGTCGATGTTAC 57.970 45.455 0.00 0.00 41.17 2.50
733 763 3.191581 TCAGTCAACCGAGACTTCATCTC 59.808 47.826 2.94 0.00 46.26 2.75
734 764 3.157881 TCAGTCAACCGAGACTTCATCT 58.842 45.455 2.94 0.00 46.26 2.90
735 765 3.191581 TCTCAGTCAACCGAGACTTCATC 59.808 47.826 2.94 0.00 46.26 2.92
738 768 3.859411 ATCTCAGTCAACCGAGACTTC 57.141 47.619 0.00 0.00 46.26 3.01
741 771 3.860536 GCTAAATCTCAGTCAACCGAGAC 59.139 47.826 0.00 0.00 40.92 3.36
742 772 3.509967 TGCTAAATCTCAGTCAACCGAGA 59.490 43.478 0.00 0.00 42.25 4.04
749 779 4.820897 ACGTGATTGCTAAATCTCAGTCA 58.179 39.130 0.00 0.00 42.40 3.41
767 797 6.693545 TGCCACTTTACAATTTTCTTAACGTG 59.306 34.615 0.00 0.00 0.00 4.49
768 798 6.797454 TGCCACTTTACAATTTTCTTAACGT 58.203 32.000 0.00 0.00 0.00 3.99
882 913 0.673333 TGGATTTGCATCGCAGTCGT 60.673 50.000 0.00 0.00 40.61 4.34
883 914 0.247814 GTGGATTTGCATCGCAGTCG 60.248 55.000 0.00 0.00 40.61 4.18
966 1006 3.181437 TGGATGGATGGATGGATCAACTG 60.181 47.826 0.00 0.00 0.00 3.16
968 1008 3.513909 TGGATGGATGGATGGATCAAC 57.486 47.619 0.00 0.00 0.00 3.18
969 1009 3.658705 TGATGGATGGATGGATGGATCAA 59.341 43.478 0.00 0.00 0.00 2.57
977 1017 3.074985 GGAGGAATTGATGGATGGATGGA 59.925 47.826 0.00 0.00 0.00 3.41
1069 1109 2.741211 GTTTCGCGTGGGGAGGAC 60.741 66.667 5.77 0.00 0.00 3.85
1083 1123 3.050275 GCGAAGAGGCTGCCGTTT 61.050 61.111 13.96 11.64 0.00 3.60
1141 1181 1.918467 TAGAGGAGGGCGACGGAGAA 61.918 60.000 0.00 0.00 0.00 2.87
1222 1262 1.316651 GCCGGGTAGAAGTCGTAGAT 58.683 55.000 2.18 0.00 40.67 1.98
1223 1263 1.091771 CGCCGGGTAGAAGTCGTAGA 61.092 60.000 2.18 0.00 0.00 2.59
1584 1660 0.622154 AGAGGAGGACGAGGAGGAGA 60.622 60.000 0.00 0.00 0.00 3.71
1840 1958 3.578716 GACGGGAGAAGATATCCATGGAA 59.421 47.826 20.67 8.82 38.70 3.53
1953 2071 1.359848 ACCTAGCTTGTTTCATCGCG 58.640 50.000 0.00 0.00 0.00 5.87
1954 2072 2.285488 GCTACCTAGCTTGTTTCATCGC 59.715 50.000 0.00 0.00 45.62 4.58
1971 2089 9.547753 TGTTCAGATCATAAAGGATTTAGCTAC 57.452 33.333 0.00 0.00 44.82 3.58
1986 2105 5.104402 TGGGTGTCATACATGTTCAGATCAT 60.104 40.000 2.30 0.00 0.00 2.45
1991 2110 3.942829 AGTGGGTGTCATACATGTTCAG 58.057 45.455 2.30 0.00 0.00 3.02
1996 2115 3.541996 TGCTAGTGGGTGTCATACATG 57.458 47.619 0.00 0.00 0.00 3.21
2019 2138 1.326245 GTTGCAACGCACGAGCATATA 59.674 47.619 14.90 0.15 38.71 0.86
2074 2311 9.793252 GCTCATATTTTATGGTATTAAGCCATG 57.207 33.333 19.07 7.10 45.47 3.66
2092 2329 8.627403 CATGTTAAAACAGAGGATGCTCATATT 58.373 33.333 17.24 8.15 43.04 1.28
2169 2417 3.011818 GTGATCATGTGGACATTGCAGA 58.988 45.455 0.00 0.00 33.61 4.26
2203 2451 5.103515 AGCTCATATTCTTGGGGTTTACCAT 60.104 40.000 0.69 0.00 40.91 3.55
2218 2466 2.648059 GTGCAGTGGGAAGCTCATATT 58.352 47.619 0.00 0.00 0.00 1.28
2219 2467 1.473965 CGTGCAGTGGGAAGCTCATAT 60.474 52.381 0.00 0.00 0.00 1.78
2358 4491 4.872691 CGTTCATGAAGTCTTCTATGCCTT 59.127 41.667 8.80 0.00 0.00 4.35
2361 4494 3.001736 GGCGTTCATGAAGTCTTCTATGC 59.998 47.826 8.80 11.80 0.00 3.14
2366 4499 3.851098 AGTAGGCGTTCATGAAGTCTTC 58.149 45.455 8.80 5.58 0.00 2.87
2504 4719 8.647143 ATCGCGAATTTCAAAATTTATTCCAT 57.353 26.923 15.24 0.00 38.64 3.41
2704 5402 2.983192 TCCAGCCATATCCGGGAATTTA 59.017 45.455 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.