Multiple sequence alignment - TraesCS6D01G089200

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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 TraesCS6D01G089200 chr6D 100.000 3586 0 0 1 3586 54237535 54241120 0.000000e+00 6623
1 TraesCS6D01G089200 chr6D 90.201 745 60 9 2846 3586 462397163 462396428 0.000000e+00 959
2 TraesCS6D01G089200 chr6D 82.920 363 37 15 1693 2046 54021614 54021960 1.620000e-78 303
3 TraesCS6D01G089200 chr6A 92.125 2184 95 24 690 2844 61007903 61005768 0.000000e+00 3009
4 TraesCS6D01G089200 chr6A 76.656 634 56 23 17 628 61008492 61007929 2.120000e-67 267
5 TraesCS6D01G089200 chr6B 90.551 2233 104 43 655 2844 116747867 116745699 0.000000e+00 2856
6 TraesCS6D01G089200 chr2D 86.295 1919 195 32 726 2608 395558800 395556914 0.000000e+00 2025
7 TraesCS6D01G089200 chr2D 90.470 745 67 4 2844 3586 136839431 136838689 0.000000e+00 979
8 TraesCS6D01G089200 chr2D 89.467 750 76 3 2839 3586 601402133 601402881 0.000000e+00 944
9 TraesCS6D01G089200 chr2B 88.327 1482 145 15 1114 2582 468552658 468551192 0.000000e+00 1753
10 TraesCS6D01G089200 chr2B 86.957 368 38 6 722 1088 468553082 468552724 4.310000e-109 405
11 TraesCS6D01G089200 chr2A 87.202 1344 140 20 1275 2608 533831574 533830253 0.000000e+00 1500
12 TraesCS6D01G089200 chr2A 89.130 368 27 6 722 1088 533837320 533836965 2.540000e-121 446
13 TraesCS6D01G089200 chr2A 95.000 160 8 0 1110 1269 533836898 533836739 5.940000e-63 252
14 TraesCS6D01G089200 chr5D 93.108 740 49 2 2844 3582 502588866 502589604 0.000000e+00 1083
15 TraesCS6D01G089200 chr1D 93.108 740 49 2 2845 3582 389432791 389433530 0.000000e+00 1083
16 TraesCS6D01G089200 chr1D 91.398 744 56 6 2845 3586 346375266 346376003 0.000000e+00 1013
17 TraesCS6D01G089200 chr4D 92.703 740 52 2 2844 3582 384677786 384678524 0.000000e+00 1066
18 TraesCS6D01G089200 chr4D 90.591 744 53 6 2840 3582 503904099 503903372 0.000000e+00 970
19 TraesCS6D01G089200 chr7A 89.544 746 68 8 2844 3586 472628300 472629038 0.000000e+00 937
20 TraesCS6D01G089200 chr5A 78.481 395 70 15 1119 1504 365253857 365254245 9.950000e-61 244
21 TraesCS6D01G089200 chr5A 77.411 394 76 12 1119 1504 365599789 365600177 4.660000e-54 222
22 TraesCS6D01G089200 chr5B 77.157 394 77 12 1119 1504 314276967 314277355 2.170000e-52 217
23 TraesCS6D01G089200 chr5B 76.962 395 76 15 1119 1504 314193696 314193308 1.010000e-50 211


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 TraesCS6D01G089200 chr6D 54237535 54241120 3585 False 6623 6623 100.0000 1 3586 1 chr6D.!!$F2 3585
1 TraesCS6D01G089200 chr6D 462396428 462397163 735 True 959 959 90.2010 2846 3586 1 chr6D.!!$R1 740
2 TraesCS6D01G089200 chr6A 61005768 61008492 2724 True 1638 3009 84.3905 17 2844 2 chr6A.!!$R1 2827
3 TraesCS6D01G089200 chr6B 116745699 116747867 2168 True 2856 2856 90.5510 655 2844 1 chr6B.!!$R1 2189
4 TraesCS6D01G089200 chr2D 395556914 395558800 1886 True 2025 2025 86.2950 726 2608 1 chr2D.!!$R2 1882
5 TraesCS6D01G089200 chr2D 136838689 136839431 742 True 979 979 90.4700 2844 3586 1 chr2D.!!$R1 742
6 TraesCS6D01G089200 chr2D 601402133 601402881 748 False 944 944 89.4670 2839 3586 1 chr2D.!!$F1 747
7 TraesCS6D01G089200 chr2B 468551192 468553082 1890 True 1079 1753 87.6420 722 2582 2 chr2B.!!$R1 1860
8 TraesCS6D01G089200 chr2A 533830253 533831574 1321 True 1500 1500 87.2020 1275 2608 1 chr2A.!!$R1 1333
9 TraesCS6D01G089200 chr2A 533836739 533837320 581 True 349 446 92.0650 722 1269 2 chr2A.!!$R2 547
10 TraesCS6D01G089200 chr5D 502588866 502589604 738 False 1083 1083 93.1080 2844 3582 1 chr5D.!!$F1 738
11 TraesCS6D01G089200 chr1D 389432791 389433530 739 False 1083 1083 93.1080 2845 3582 1 chr1D.!!$F2 737
12 TraesCS6D01G089200 chr1D 346375266 346376003 737 False 1013 1013 91.3980 2845 3586 1 chr1D.!!$F1 741
13 TraesCS6D01G089200 chr4D 384677786 384678524 738 False 1066 1066 92.7030 2844 3582 1 chr4D.!!$F1 738
14 TraesCS6D01G089200 chr4D 503903372 503904099 727 True 970 970 90.5910 2840 3582 1 chr4D.!!$R1 742
15 TraesCS6D01G089200 chr7A 472628300 472629038 738 False 937 937 89.5440 2844 3586 1 chr7A.!!$F1 742

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
497 543 0.116342 TTGCTGTAGACTCCCCCTCA 59.884 55.0 0.0 0.0 0.0 3.86 F
1050 1116 0.039764 ACCGATGTCTCCAGTCTCCA 59.960 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2263 0.736325 AGGCGACGTACTGCATGTTC 60.736 55.0 8.85 0.0 0.0 3.18 R
2972 3136 1.153353 GCCGATTTGGACGTTTCTCA 58.847 50.0 0.00 0.0 42.0 3.27 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
35 36 8.809159 TCATTGTTTTTAAAATGAGATCGCAA 57.191 26.923 2.39 0.00 37.76 4.85
36 37 9.421806 TCATTGTTTTTAAAATGAGATCGCAAT 57.578 25.926 2.39 0.00 37.76 3.56
39 40 7.508965 TGTTTTTAAAATGAGATCGCAATTGC 58.491 30.769 20.76 20.76 37.78 3.56
40 41 7.170489 TGTTTTTAAAATGAGATCGCAATTGCA 59.830 29.630 28.77 16.65 42.21 4.08
41 42 6.874297 TTTAAAATGAGATCGCAATTGCAG 57.126 33.333 28.77 20.64 42.21 4.41
42 43 4.707030 AAAATGAGATCGCAATTGCAGA 57.293 36.364 28.77 24.59 42.21 4.26
43 44 3.687572 AATGAGATCGCAATTGCAGAC 57.312 42.857 28.77 17.97 42.21 3.51
44 45 2.391616 TGAGATCGCAATTGCAGACT 57.608 45.000 28.77 21.88 42.21 3.24
45 46 2.703416 TGAGATCGCAATTGCAGACTT 58.297 42.857 28.77 17.06 42.21 3.01
46 47 3.076621 TGAGATCGCAATTGCAGACTTT 58.923 40.909 28.77 15.01 42.21 2.66
47 48 3.503363 TGAGATCGCAATTGCAGACTTTT 59.497 39.130 28.77 12.25 42.21 2.27
54 55 5.404968 TCGCAATTGCAGACTTTTAAAATGG 59.595 36.000 28.77 7.74 42.21 3.16
77 104 4.322650 GGGTTGCAAGGCATTTCTCAAATA 60.323 41.667 0.00 0.00 38.76 1.40
80 107 3.448301 TGCAAGGCATTTCTCAAATAGGG 59.552 43.478 0.00 0.00 31.71 3.53
82 109 4.678840 GCAAGGCATTTCTCAAATAGGGTG 60.679 45.833 0.00 0.00 0.00 4.61
105 132 6.234920 TGGCAACAGCATACTTTAAAGTAGA 58.765 36.000 27.21 12.68 46.17 2.59
156 183 5.534654 TCACAACTGTAAGATTTCAAAGGGG 59.465 40.000 0.00 0.00 37.43 4.79
163 190 4.980339 AAGATTTCAAAGGGGTTGCAAT 57.020 36.364 0.59 0.00 36.01 3.56
184 211 8.760103 GCAATTGCAATTTTTAAATGGGATTT 57.240 26.923 25.36 0.00 41.59 2.17
185 212 8.862074 GCAATTGCAATTTTTAAATGGGATTTC 58.138 29.630 25.36 0.00 41.59 2.17
186 213 9.909644 CAATTGCAATTTTTAAATGGGATTTCA 57.090 25.926 21.95 0.00 33.82 2.69
203 230 6.594937 GGGATTTCAGCTGCAATTTTTCATAA 59.405 34.615 12.94 0.00 0.00 1.90
213 240 8.385858 GCTGCAATTTTTCATAATTTTCTCTCC 58.614 33.333 0.00 0.00 0.00 3.71
214 241 9.426837 CTGCAATTTTTCATAATTTTCTCTCCA 57.573 29.630 0.00 0.00 0.00 3.86
231 258 6.644347 TCTCTCCATTTCATACTTTCTGTCC 58.356 40.000 0.00 0.00 0.00 4.02
232 259 6.441924 TCTCTCCATTTCATACTTTCTGTCCT 59.558 38.462 0.00 0.00 0.00 3.85
233 260 7.020827 TCTCCATTTCATACTTTCTGTCCTT 57.979 36.000 0.00 0.00 0.00 3.36
236 263 8.477419 TCCATTTCATACTTTCTGTCCTTTTT 57.523 30.769 0.00 0.00 0.00 1.94
260 287 3.831323 TGTCAACCACATGGAAATGACT 58.169 40.909 23.55 0.00 42.00 3.41
276 303 7.541122 GAAATGACTTCCTAAGCGAAATAGT 57.459 36.000 0.00 0.00 0.00 2.12
277 304 8.644318 GAAATGACTTCCTAAGCGAAATAGTA 57.356 34.615 0.00 0.00 0.00 1.82
278 305 8.421673 AAATGACTTCCTAAGCGAAATAGTAC 57.578 34.615 0.00 0.00 0.00 2.73
279 306 6.770746 TGACTTCCTAAGCGAAATAGTACT 57.229 37.500 0.00 0.00 0.00 2.73
280 307 7.166691 TGACTTCCTAAGCGAAATAGTACTT 57.833 36.000 0.00 0.00 0.00 2.24
281 308 8.284945 TGACTTCCTAAGCGAAATAGTACTTA 57.715 34.615 0.00 0.00 0.00 2.24
287 314 8.186821 TCCTAAGCGAAATAGTACTTACTTGAC 58.813 37.037 0.00 0.00 37.73 3.18
289 316 5.338365 AGCGAAATAGTACTTACTTGACGG 58.662 41.667 0.00 0.00 37.73 4.79
296 323 5.857822 AGTACTTACTTGACGGAAAATGC 57.142 39.130 0.00 0.00 31.13 3.56
303 330 8.357402 ACTTACTTGACGGAAAATGCTTATTTT 58.643 29.630 0.00 0.00 36.54 1.82
308 335 8.600449 TTGACGGAAAATGCTTATTTTTCATT 57.400 26.923 10.12 0.00 42.28 2.57
314 341 7.066163 GGAAAATGCTTATTTTTCATTGAGGGG 59.934 37.037 10.12 0.00 42.28 4.79
315 342 6.872585 AATGCTTATTTTTCATTGAGGGGA 57.127 33.333 0.00 0.00 0.00 4.81
316 343 6.872585 ATGCTTATTTTTCATTGAGGGGAA 57.127 33.333 0.00 0.00 0.00 3.97
329 356 4.693042 TGAGGGGAACGTTTCTCTTTTA 57.307 40.909 11.15 0.00 0.00 1.52
330 357 5.038651 TGAGGGGAACGTTTCTCTTTTAA 57.961 39.130 11.15 0.00 0.00 1.52
331 358 5.438833 TGAGGGGAACGTTTCTCTTTTAAA 58.561 37.500 11.15 0.00 0.00 1.52
332 359 5.887035 TGAGGGGAACGTTTCTCTTTTAAAA 59.113 36.000 11.15 0.00 0.00 1.52
337 364 9.701098 GGGGAACGTTTCTCTTTTAAAATAATT 57.299 29.630 6.53 0.00 0.00 1.40
415 450 7.038302 TCACTTTCTTCTAGTCATTACCCATGT 60.038 37.037 0.00 0.00 34.06 3.21
423 458 5.755409 AGTCATTACCCATGTGTTCAGTA 57.245 39.130 0.00 0.00 34.06 2.74
454 500 5.532406 CAGCAGGCCTAATATACAATGTGTT 59.468 40.000 3.98 0.00 0.00 3.32
486 532 9.515020 TTTTTATTTGTCTTTCAGTTGCTGTAG 57.485 29.630 0.00 0.00 32.61 2.74
487 533 8.445275 TTTATTTGTCTTTCAGTTGCTGTAGA 57.555 30.769 0.00 0.00 32.61 2.59
488 534 5.734855 TTTGTCTTTCAGTTGCTGTAGAC 57.265 39.130 18.03 18.03 40.67 2.59
489 535 4.672587 TGTCTTTCAGTTGCTGTAGACT 57.327 40.909 21.68 0.00 40.77 3.24
490 536 4.621991 TGTCTTTCAGTTGCTGTAGACTC 58.378 43.478 21.68 8.63 40.77 3.36
491 537 3.991121 GTCTTTCAGTTGCTGTAGACTCC 59.009 47.826 17.80 3.03 39.09 3.85
492 538 3.006967 TCTTTCAGTTGCTGTAGACTCCC 59.993 47.826 0.00 0.00 32.61 4.30
493 539 1.267121 TCAGTTGCTGTAGACTCCCC 58.733 55.000 0.00 0.00 32.61 4.81
494 540 0.250513 CAGTTGCTGTAGACTCCCCC 59.749 60.000 0.00 0.00 0.00 5.40
495 541 0.117340 AGTTGCTGTAGACTCCCCCT 59.883 55.000 0.00 0.00 0.00 4.79
496 542 0.537653 GTTGCTGTAGACTCCCCCTC 59.462 60.000 0.00 0.00 0.00 4.30
497 543 0.116342 TTGCTGTAGACTCCCCCTCA 59.884 55.000 0.00 0.00 0.00 3.86
498 544 0.116342 TGCTGTAGACTCCCCCTCAA 59.884 55.000 0.00 0.00 0.00 3.02
499 545 1.276622 GCTGTAGACTCCCCCTCAAA 58.723 55.000 0.00 0.00 0.00 2.69
500 546 1.628846 GCTGTAGACTCCCCCTCAAAA 59.371 52.381 0.00 0.00 0.00 2.44
501 547 2.039879 GCTGTAGACTCCCCCTCAAAAA 59.960 50.000 0.00 0.00 0.00 1.94
540 586 8.727910 CAAACTAACCAACTATAACTCTTTCCC 58.272 37.037 0.00 0.00 0.00 3.97
549 595 5.796399 ACTATAACTCTTTCCCCCTCCTTTT 59.204 40.000 0.00 0.00 0.00 2.27
565 611 4.365723 TCCTTTTCTTGTACGAGTGACAC 58.634 43.478 10.00 0.00 0.00 3.67
570 616 6.483385 TTTCTTGTACGAGTGACACAAAAA 57.517 33.333 8.59 0.00 32.16 1.94
593 639 5.722021 AAAGACACAACAGGAAACAAACT 57.278 34.783 0.00 0.00 0.00 2.66
654 701 9.453572 AACATGATATTAGCTGTTCTCTTTTGA 57.546 29.630 0.00 0.00 0.00 2.69
655 702 9.453572 ACATGATATTAGCTGTTCTCTTTTGAA 57.546 29.630 0.00 0.00 0.00 2.69
843 909 4.430423 CGCGCGGCTGTGTTTCTC 62.430 66.667 24.84 0.00 0.00 2.87
859 925 3.114647 CTCGCCTTCTCCCTCGTCG 62.115 68.421 0.00 0.00 0.00 5.12
860 926 3.441290 CGCCTTCTCCCTCGTCGT 61.441 66.667 0.00 0.00 0.00 4.34
861 927 2.490685 GCCTTCTCCCTCGTCGTC 59.509 66.667 0.00 0.00 0.00 4.20
871 937 1.134901 CTCGTCGTCTGGTTCTCCG 59.865 63.158 0.00 0.00 36.30 4.63
888 954 3.474570 GGCCATGTCCTCGCCTCT 61.475 66.667 0.00 0.00 39.70 3.69
946 1012 1.077858 CTCTTCTTCCAGGGCCAGC 60.078 63.158 6.18 0.00 0.00 4.85
984 1050 2.426023 GACCAGGCCGTCAAGTGT 59.574 61.111 5.95 0.00 32.74 3.55
985 1051 1.227853 GACCAGGCCGTCAAGTGTT 60.228 57.895 5.95 0.00 32.74 3.32
1032 1098 2.725815 GCCGCAAACGTGAGCAAC 60.726 61.111 12.24 0.67 37.70 4.17
1044 1110 0.247460 TGAGCAACCGATGTCTCCAG 59.753 55.000 0.00 0.00 33.75 3.86
1046 1112 0.247736 AGCAACCGATGTCTCCAGTC 59.752 55.000 0.00 0.00 0.00 3.51
1048 1114 1.737363 GCAACCGATGTCTCCAGTCTC 60.737 57.143 0.00 0.00 0.00 3.36
1050 1116 0.039764 ACCGATGTCTCCAGTCTCCA 59.960 55.000 0.00 0.00 0.00 3.86
1302 1414 4.521062 CCTCCTGAAGGCGGCGAG 62.521 72.222 12.98 3.41 38.67 5.03
1544 1656 2.227089 GAGGGACGTGATGGCGTTCT 62.227 60.000 0.00 0.00 45.79 3.01
1674 1790 4.268405 AGTGCAACGAATTGAAAAGCTTTG 59.732 37.500 13.54 0.34 45.86 2.77
1711 1828 1.519758 ACGTGTTTCTTGTAACGAGCG 59.480 47.619 0.57 0.00 39.27 5.03
1795 1912 1.853963 ACAGCTCCTACCTCAACGAT 58.146 50.000 0.00 0.00 0.00 3.73
2573 2725 3.145551 GCCTACTTCGCCGGGAGA 61.146 66.667 2.18 0.00 0.00 3.71
2597 2749 4.988598 AACTGACCACCGCTGCCG 62.989 66.667 0.00 0.00 0.00 5.69
2605 2757 4.760047 ACCGCTGCCGTGTGGATC 62.760 66.667 7.84 0.00 39.82 3.36
2606 2758 4.457496 CCGCTGCCGTGTGGATCT 62.457 66.667 0.00 0.00 39.82 2.75
2608 2760 1.153647 CGCTGCCGTGTGGATCTTA 60.154 57.895 0.00 0.00 37.49 2.10
2609 2761 0.739462 CGCTGCCGTGTGGATCTTAA 60.739 55.000 0.00 0.00 37.49 1.85
2686 2841 7.828508 ACATCATTAATCATGGCAGTACAAT 57.171 32.000 4.24 0.00 33.07 2.71
2701 2856 7.118245 TGGCAGTACAATCGATGATTAATGATC 59.882 37.037 0.00 4.93 30.44 2.92
2836 2996 4.333690 AGGCATATGAAAGGATGATGAGC 58.666 43.478 6.97 0.00 0.00 4.26
2966 3130 0.179015 TTAAAGCACGTCCAGGCCAA 60.179 50.000 5.01 0.00 0.00 4.52
2972 3136 2.270205 CGTCCAGGCCAAGCTCAT 59.730 61.111 5.01 0.00 0.00 2.90
2993 3157 0.872388 AGAAACGTCCAAATCGGCAC 59.128 50.000 0.00 0.00 33.14 5.01
3042 3206 2.203538 AAGGTGGGCCACTTGCAG 60.204 61.111 33.87 0.00 43.89 4.41
3048 3212 3.650950 GGCCACTTGCAGGAGGGA 61.651 66.667 13.99 0.00 43.89 4.20
3058 3222 0.692419 GCAGGAGGGAAGATGGGAGA 60.692 60.000 0.00 0.00 0.00 3.71
3101 3265 1.929836 GTGCGTGCTTATCTTCTCCTG 59.070 52.381 0.00 0.00 0.00 3.86
3114 3278 0.116342 TCTCCTGCCTCCAGTAACCA 59.884 55.000 0.00 0.00 37.38 3.67
3178 3342 1.269102 CGGTGCTTCGATTCGAGGTAT 60.269 52.381 17.90 0.00 37.14 2.73
3203 3367 5.142061 TCTACACGAAAAAGATGCACCTA 57.858 39.130 0.00 0.00 0.00 3.08
3461 3626 2.261671 GACACCGCCATGTCGAGT 59.738 61.111 0.00 0.00 39.69 4.18
3510 3675 3.054503 CGTCCCTCTCGACACCGT 61.055 66.667 0.00 0.00 37.05 4.83
3557 3722 4.260170 CCACGTCCTACTACACTAGAGTT 58.740 47.826 0.00 0.00 0.00 3.01
3563 3728 6.072838 CGTCCTACTACACTAGAGTTGTTTCA 60.073 42.308 11.95 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.809159 TTGCGATCTCATTTTAAAAACAATGA 57.191 26.923 4.44 3.47 37.12 2.57
13 14 8.008844 GCAATTGCGATCTCATTTTAAAAACAA 58.991 29.630 15.87 1.27 0.00 2.83
14 15 7.170489 TGCAATTGCGATCTCATTTTAAAAACA 59.830 29.630 24.58 0.00 45.83 2.83
15 16 7.508965 TGCAATTGCGATCTCATTTTAAAAAC 58.491 30.769 24.58 0.00 45.83 2.43
16 17 7.598118 TCTGCAATTGCGATCTCATTTTAAAAA 59.402 29.630 24.58 0.69 45.83 1.94
17 18 7.062138 GTCTGCAATTGCGATCTCATTTTAAAA 59.938 33.333 24.58 2.51 45.83 1.52
18 19 6.527722 GTCTGCAATTGCGATCTCATTTTAAA 59.472 34.615 24.58 1.72 45.83 1.52
19 20 6.029607 GTCTGCAATTGCGATCTCATTTTAA 58.970 36.000 24.58 2.16 45.83 1.52
20 21 5.355071 AGTCTGCAATTGCGATCTCATTTTA 59.645 36.000 24.58 2.36 45.83 1.52
21 22 4.157289 AGTCTGCAATTGCGATCTCATTTT 59.843 37.500 24.58 0.30 45.83 1.82
22 23 3.693085 AGTCTGCAATTGCGATCTCATTT 59.307 39.130 24.58 1.57 45.83 2.32
23 24 3.276857 AGTCTGCAATTGCGATCTCATT 58.723 40.909 24.58 3.00 45.83 2.57
24 25 2.915349 AGTCTGCAATTGCGATCTCAT 58.085 42.857 24.58 4.86 45.83 2.90
25 26 2.391616 AGTCTGCAATTGCGATCTCA 57.608 45.000 24.58 5.84 45.83 3.27
26 27 3.754188 AAAGTCTGCAATTGCGATCTC 57.246 42.857 24.58 12.97 45.83 2.75
27 28 5.627499 TTAAAAGTCTGCAATTGCGATCT 57.373 34.783 24.58 18.01 45.83 2.75
28 29 6.689178 TTTTAAAAGTCTGCAATTGCGATC 57.311 33.333 24.58 16.21 45.83 3.69
29 30 6.091169 CCATTTTAAAAGTCTGCAATTGCGAT 59.909 34.615 24.58 12.08 45.83 4.58
30 31 5.404968 CCATTTTAAAAGTCTGCAATTGCGA 59.595 36.000 24.58 20.45 45.83 5.10
31 32 5.389725 CCCATTTTAAAAGTCTGCAATTGCG 60.390 40.000 24.58 18.63 45.83 4.85
32 33 5.106594 CCCCATTTTAAAAGTCTGCAATTGC 60.107 40.000 23.69 23.69 42.50 3.56
33 34 5.997129 ACCCCATTTTAAAAGTCTGCAATTG 59.003 36.000 6.79 0.00 0.00 2.32
34 35 6.186420 ACCCCATTTTAAAAGTCTGCAATT 57.814 33.333 6.79 0.00 0.00 2.32
35 36 5.823861 ACCCCATTTTAAAAGTCTGCAAT 57.176 34.783 6.79 0.00 0.00 3.56
36 37 5.363939 CAACCCCATTTTAAAAGTCTGCAA 58.636 37.500 6.79 0.00 0.00 4.08
37 38 4.742138 GCAACCCCATTTTAAAAGTCTGCA 60.742 41.667 6.79 0.00 0.00 4.41
38 39 3.745975 GCAACCCCATTTTAAAAGTCTGC 59.254 43.478 6.79 5.81 0.00 4.26
39 40 4.954875 TGCAACCCCATTTTAAAAGTCTG 58.045 39.130 6.79 0.23 0.00 3.51
40 41 5.454613 CCTTGCAACCCCATTTTAAAAGTCT 60.455 40.000 6.79 0.00 0.00 3.24
41 42 4.754618 CCTTGCAACCCCATTTTAAAAGTC 59.245 41.667 6.79 0.00 0.00 3.01
42 43 4.713553 CCTTGCAACCCCATTTTAAAAGT 58.286 39.130 6.79 0.00 0.00 2.66
43 44 3.501828 GCCTTGCAACCCCATTTTAAAAG 59.498 43.478 6.79 0.00 0.00 2.27
44 45 3.117888 TGCCTTGCAACCCCATTTTAAAA 60.118 39.130 2.51 2.51 34.76 1.52
45 46 2.439507 TGCCTTGCAACCCCATTTTAAA 59.560 40.909 0.00 0.00 34.76 1.52
46 47 2.050144 TGCCTTGCAACCCCATTTTAA 58.950 42.857 0.00 0.00 34.76 1.52
47 48 1.722034 TGCCTTGCAACCCCATTTTA 58.278 45.000 0.00 0.00 34.76 1.52
54 55 0.968405 TGAGAAATGCCTTGCAACCC 59.032 50.000 0.00 0.00 43.62 4.11
77 104 0.405585 AAGTATGCTGTTGCCACCCT 59.594 50.000 0.00 0.00 38.71 4.34
80 107 5.121221 ACTTTAAAGTATGCTGTTGCCAC 57.879 39.130 19.26 0.00 37.52 5.01
82 109 6.675728 GCTCTACTTTAAAGTATGCTGTTGCC 60.676 42.308 27.92 11.35 40.46 4.52
88 115 7.545489 AGTTACGCTCTACTTTAAAGTATGCT 58.455 34.615 29.72 23.55 40.46 3.79
105 132 7.279313 TCTCACTTCAAAACTTAAAGTTACGCT 59.721 33.333 0.00 0.00 37.47 5.07
123 150 7.897575 AATCTTACAGTTGTGATCTCACTTC 57.102 36.000 11.35 4.96 46.55 3.01
138 165 4.280677 TGCAACCCCTTTGAAATCTTACAG 59.719 41.667 0.00 0.00 37.39 2.74
163 190 7.447853 AGCTGAAATCCCATTTAAAAATTGCAA 59.552 29.630 0.00 0.00 31.47 4.08
169 196 5.862845 TGCAGCTGAAATCCCATTTAAAAA 58.137 33.333 20.43 0.00 31.47 1.94
170 197 5.480642 TGCAGCTGAAATCCCATTTAAAA 57.519 34.783 20.43 0.00 31.47 1.52
171 198 5.480642 TTGCAGCTGAAATCCCATTTAAA 57.519 34.783 20.43 0.00 31.47 1.52
172 199 5.680594 ATTGCAGCTGAAATCCCATTTAA 57.319 34.783 20.43 0.00 31.47 1.52
173 200 5.680594 AATTGCAGCTGAAATCCCATTTA 57.319 34.783 20.53 0.00 31.47 1.40
174 201 4.563140 AATTGCAGCTGAAATCCCATTT 57.437 36.364 20.53 1.43 34.64 2.32
175 202 4.563140 AAATTGCAGCTGAAATCCCATT 57.437 36.364 20.53 8.25 0.00 3.16
176 203 4.563140 AAAATTGCAGCTGAAATCCCAT 57.437 36.364 20.53 1.70 0.00 4.00
177 204 4.202336 TGAAAAATTGCAGCTGAAATCCCA 60.202 37.500 20.53 12.39 0.00 4.37
178 205 4.317488 TGAAAAATTGCAGCTGAAATCCC 58.683 39.130 20.53 10.14 0.00 3.85
179 206 7.599630 TTATGAAAAATTGCAGCTGAAATCC 57.400 32.000 20.53 10.46 0.00 3.01
182 209 9.881529 GAAAATTATGAAAAATTGCAGCTGAAA 57.118 25.926 20.43 15.35 0.00 2.69
183 210 9.275398 AGAAAATTATGAAAAATTGCAGCTGAA 57.725 25.926 20.43 2.96 0.00 3.02
184 211 8.836268 AGAAAATTATGAAAAATTGCAGCTGA 57.164 26.923 20.43 0.00 0.00 4.26
185 212 8.932791 AGAGAAAATTATGAAAAATTGCAGCTG 58.067 29.630 10.11 10.11 0.00 4.24
186 213 9.148104 GAGAGAAAATTATGAAAAATTGCAGCT 57.852 29.630 0.00 0.00 0.00 4.24
187 214 8.385858 GGAGAGAAAATTATGAAAAATTGCAGC 58.614 33.333 0.00 0.00 0.00 5.25
203 230 9.525826 ACAGAAAGTATGAAATGGAGAGAAAAT 57.474 29.630 0.00 0.00 0.00 1.82
207 234 6.441924 AGGACAGAAAGTATGAAATGGAGAGA 59.558 38.462 0.00 0.00 0.00 3.10
236 263 5.128499 AGTCATTTCCATGTGGTTGACAAAA 59.872 36.000 22.14 8.59 40.08 2.44
237 264 4.648762 AGTCATTTCCATGTGGTTGACAAA 59.351 37.500 22.14 9.11 40.08 2.83
238 265 4.214310 AGTCATTTCCATGTGGTTGACAA 58.786 39.130 22.14 0.00 40.08 3.18
239 266 3.831323 AGTCATTTCCATGTGGTTGACA 58.169 40.909 22.14 0.00 40.08 3.58
240 267 4.798574 GAAGTCATTTCCATGTGGTTGAC 58.201 43.478 17.04 17.04 39.06 3.18
260 287 8.742777 TCAAGTAAGTACTATTTCGCTTAGGAA 58.257 33.333 0.00 0.00 34.99 3.36
267 294 5.335127 TCCGTCAAGTAAGTACTATTTCGC 58.665 41.667 0.00 0.00 34.99 4.70
272 299 7.328737 AGCATTTTCCGTCAAGTAAGTACTAT 58.671 34.615 0.00 0.00 34.99 2.12
273 300 6.694447 AGCATTTTCCGTCAAGTAAGTACTA 58.306 36.000 0.00 0.00 34.99 1.82
274 301 5.548406 AGCATTTTCCGTCAAGTAAGTACT 58.452 37.500 0.00 0.00 38.39 2.73
275 302 5.857822 AGCATTTTCCGTCAAGTAAGTAC 57.142 39.130 0.00 0.00 0.00 2.73
276 303 8.556213 AATAAGCATTTTCCGTCAAGTAAGTA 57.444 30.769 0.00 0.00 0.00 2.24
277 304 7.448748 AATAAGCATTTTCCGTCAAGTAAGT 57.551 32.000 0.00 0.00 0.00 2.24
278 305 8.742554 AAAATAAGCATTTTCCGTCAAGTAAG 57.257 30.769 0.00 0.00 39.63 2.34
279 306 9.187455 GAAAAATAAGCATTTTCCGTCAAGTAA 57.813 29.630 0.00 0.00 42.29 2.24
280 307 8.353684 TGAAAAATAAGCATTTTCCGTCAAGTA 58.646 29.630 8.71 0.00 42.29 2.24
281 308 7.206687 TGAAAAATAAGCATTTTCCGTCAAGT 58.793 30.769 8.71 0.00 42.29 3.16
287 314 7.201548 CCCTCAATGAAAAATAAGCATTTTCCG 60.202 37.037 8.71 0.18 42.29 4.30
289 316 7.823799 TCCCCTCAATGAAAAATAAGCATTTTC 59.176 33.333 5.11 5.11 42.29 2.29
296 323 6.267496 ACGTTCCCCTCAATGAAAAATAAG 57.733 37.500 0.00 0.00 0.00 1.73
303 330 3.072476 AGAGAAACGTTCCCCTCAATGAA 59.928 43.478 20.17 0.00 0.00 2.57
308 335 3.570912 AAAAGAGAAACGTTCCCCTCA 57.429 42.857 20.17 0.00 0.00 3.86
344 371 7.917003 TCCATAGCAGGCTATAACATGAATTA 58.083 34.615 13.07 0.00 37.16 1.40
346 373 6.378661 TCCATAGCAGGCTATAACATGAAT 57.621 37.500 13.07 0.00 37.16 2.57
362 389 4.723309 AGGATGTGAGGATTTTCCATAGC 58.277 43.478 0.00 0.00 39.61 2.97
363 390 6.599445 AGAAGGATGTGAGGATTTTCCATAG 58.401 40.000 0.00 0.00 39.61 2.23
415 450 3.691118 GCCTGCTGATGAATTACTGAACA 59.309 43.478 0.00 0.00 0.00 3.18
423 458 6.782986 TGTATATTAGGCCTGCTGATGAATT 58.217 36.000 17.99 0.00 0.00 2.17
477 523 0.537653 GAGGGGGAGTCTACAGCAAC 59.462 60.000 0.00 0.00 0.00 4.17
506 552 9.524106 GTTATAGTTGGTTAGTTTGTTTGCTTT 57.476 29.630 0.00 0.00 0.00 3.51
507 553 8.909923 AGTTATAGTTGGTTAGTTTGTTTGCTT 58.090 29.630 0.00 0.00 0.00 3.91
540 586 3.006537 TCACTCGTACAAGAAAAGGAGGG 59.993 47.826 0.00 0.00 33.37 4.30
570 616 6.015434 AGAGTTTGTTTCCTGTTGTGTCTTTT 60.015 34.615 0.00 0.00 0.00 2.27
571 617 5.476945 AGAGTTTGTTTCCTGTTGTGTCTTT 59.523 36.000 0.00 0.00 0.00 2.52
572 618 5.010282 AGAGTTTGTTTCCTGTTGTGTCTT 58.990 37.500 0.00 0.00 0.00 3.01
573 619 4.589908 AGAGTTTGTTTCCTGTTGTGTCT 58.410 39.130 0.00 0.00 0.00 3.41
574 620 4.965119 AGAGTTTGTTTCCTGTTGTGTC 57.035 40.909 0.00 0.00 0.00 3.67
575 621 5.354234 CACTAGAGTTTGTTTCCTGTTGTGT 59.646 40.000 0.00 0.00 0.00 3.72
576 622 5.354234 ACACTAGAGTTTGTTTCCTGTTGTG 59.646 40.000 0.00 0.00 35.14 3.33
577 623 5.354234 CACACTAGAGTTTGTTTCCTGTTGT 59.646 40.000 0.00 0.00 0.00 3.32
583 629 2.552743 GGCCACACTAGAGTTTGTTTCC 59.447 50.000 0.00 0.00 0.00 3.13
628 675 9.453572 TCAAAAGAGAACAGCTAATATCATGTT 57.546 29.630 0.00 0.00 38.53 2.71
651 698 9.453572 ACTGAGAACAGCTAATATCATTTTCAA 57.546 29.630 0.00 0.00 46.95 2.69
652 699 9.453572 AACTGAGAACAGCTAATATCATTTTCA 57.546 29.630 0.00 0.00 46.95 2.69
653 700 9.713740 CAACTGAGAACAGCTAATATCATTTTC 57.286 33.333 0.00 0.00 46.95 2.29
654 701 9.453572 TCAACTGAGAACAGCTAATATCATTTT 57.546 29.630 0.00 0.00 46.95 1.82
655 702 9.453572 TTCAACTGAGAACAGCTAATATCATTT 57.546 29.630 0.00 0.00 46.95 2.32
656 703 8.887717 GTTCAACTGAGAACAGCTAATATCATT 58.112 33.333 11.02 0.00 46.95 2.57
657 704 7.223582 CGTTCAACTGAGAACAGCTAATATCAT 59.776 37.037 14.47 0.00 46.32 2.45
658 705 6.531594 CGTTCAACTGAGAACAGCTAATATCA 59.468 38.462 14.47 0.00 46.32 2.15
667 714 4.556233 TGGTATCGTTCAACTGAGAACAG 58.444 43.478 14.47 0.00 46.32 3.16
827 893 4.430423 CGAGAAACACAGCCGCGC 62.430 66.667 0.00 0.00 0.00 6.86
843 909 3.398353 GACGACGAGGGAGAAGGCG 62.398 68.421 0.00 0.00 0.00 5.52
859 925 1.450312 CATGGCCGGAGAACCAGAC 60.450 63.158 5.05 0.00 37.00 3.51
860 926 1.899437 GACATGGCCGGAGAACCAGA 61.899 60.000 5.05 0.00 37.00 3.86
861 927 1.450312 GACATGGCCGGAGAACCAG 60.450 63.158 5.05 0.00 37.00 4.00
886 952 1.248785 GCGTAGTGAGGGTGTCCAGA 61.249 60.000 0.00 0.00 34.83 3.86
888 954 2.280552 GGCGTAGTGAGGGTGTCCA 61.281 63.158 0.00 0.00 34.83 4.02
925 991 1.077858 GGCCCTGGAAGAAGAGCAG 60.078 63.158 0.00 0.00 34.07 4.24
984 1050 0.327924 ACATGGCGGAGTTGGATCAA 59.672 50.000 0.00 0.00 0.00 2.57
985 1051 0.107703 GACATGGCGGAGTTGGATCA 60.108 55.000 0.00 0.00 0.00 2.92
1032 1098 0.457851 GTGGAGACTGGAGACATCGG 59.542 60.000 0.00 0.00 41.51 4.18
1044 1110 5.067544 GGATAAGTGGTACTACAGTGGAGAC 59.932 48.000 10.09 2.88 0.00 3.36
1046 1112 5.202004 AGGATAAGTGGTACTACAGTGGAG 58.798 45.833 12.29 0.00 0.00 3.86
1048 1114 5.187186 ACAAGGATAAGTGGTACTACAGTGG 59.813 44.000 12.29 0.00 0.00 4.00
1050 1116 6.282199 CACAAGGATAAGTGGTACTACAGT 57.718 41.667 12.29 1.63 32.24 3.55
1674 1790 2.091588 CACGTACGCACAAGGATTACAC 59.908 50.000 16.72 0.00 0.00 2.90
1795 1912 3.157252 GCGCCCAGGGAGATGAGA 61.157 66.667 14.69 0.00 0.00 3.27
2111 2263 0.736325 AGGCGACGTACTGCATGTTC 60.736 55.000 8.85 0.00 0.00 3.18
2573 2725 1.623811 AGCGGTGGTCAGTTCTTGTAT 59.376 47.619 0.00 0.00 0.00 2.29
2639 2794 8.754991 TGTAGTTTATTGGAAGTTTTCTTGGA 57.245 30.769 0.00 0.00 40.61 3.53
2686 2841 7.875554 TCCGGTTTATTGATCATTAATCATCGA 59.124 33.333 12.81 0.00 43.87 3.59
2785 2945 3.438434 GTGCCTCTTCCAATTCTTCTGAC 59.562 47.826 0.00 0.00 0.00 3.51
2816 2976 3.442977 GGGCTCATCATCCTTTCATATGC 59.557 47.826 0.00 0.00 0.00 3.14
2821 2981 2.309755 AGTTGGGCTCATCATCCTTTCA 59.690 45.455 0.00 0.00 0.00 2.69
2909 3071 2.174107 CACAGTGAACGCATGCCG 59.826 61.111 13.15 10.04 44.21 5.69
2910 3072 2.126734 GCACAGTGAACGCATGCC 60.127 61.111 13.15 0.00 0.00 4.40
2913 3075 3.726517 GCCGCACAGTGAACGCAT 61.727 61.111 4.15 0.00 0.00 4.73
2966 3130 2.839486 TTGGACGTTTCTCATGAGCT 57.161 45.000 18.36 0.00 0.00 4.09
2972 3136 1.153353 GCCGATTTGGACGTTTCTCA 58.847 50.000 0.00 0.00 42.00 3.27
3042 3206 2.414250 ATCTCTCCCATCTTCCCTCC 57.586 55.000 0.00 0.00 0.00 4.30
3048 3212 2.890311 CAGCTCGTATCTCTCCCATCTT 59.110 50.000 0.00 0.00 0.00 2.40
3101 3265 0.470341 GAGGGATGGTTACTGGAGGC 59.530 60.000 0.00 0.00 0.00 4.70
3114 3278 7.147461 GGTTAGGAAGAACAGAATTAGAGGGAT 60.147 40.741 0.00 0.00 0.00 3.85
3178 3342 3.186409 GTGCATCTTTTTCGTGTAGAGCA 59.814 43.478 0.00 0.00 0.00 4.26
3203 3367 2.158900 CCTGAATGGAACCGTAGCATCT 60.159 50.000 0.00 0.00 38.35 2.90
3243 3407 4.269363 CGAAATTAAGAACTTACGGCCGAT 59.731 41.667 35.90 18.92 0.00 4.18
3327 3491 4.692228 TGCTGGTCAAAGGAAAATTCAAC 58.308 39.130 0.00 0.00 0.00 3.18
3447 3612 2.264794 GGAACTCGACATGGCGGT 59.735 61.111 23.19 15.26 0.00 5.68
3461 3626 1.076187 TCTGAGCAGAGGACAGAGGAA 59.924 52.381 0.00 0.00 36.04 3.36
3510 3675 1.695989 GGAGATCAAGGGGAAGGGCTA 60.696 57.143 0.00 0.00 0.00 3.93
3557 3722 1.005037 ATGAGCGACGCCTGAAACA 60.005 52.632 17.79 7.93 0.00 2.83
3563 3728 3.893763 CCGAGATGAGCGACGCCT 61.894 66.667 17.79 6.07 0.00 5.52


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

AutoCloner maintained by Alex Coulton.