Multiple sequence alignment - TraesCS2D01G065000

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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 TraesCS2D01G065000 chr2D 100.000 2864 0 0 1 2864 27835822 27838685 0.000000e+00 5289.0
1 TraesCS2D01G065000 chr2A 93.867 2250 79 18 86 2302 29988638 29990861 0.000000e+00 3336.0
2 TraesCS2D01G065000 chr2A 94.235 451 21 1 2362 2807 29990882 29991332 0.000000e+00 684.0
3 TraesCS2D01G065000 chr2A 98.361 61 1 0 2804 2864 29999972 30000032 1.090000e-19 108.0
4 TraesCS2D01G065000 chr2A 100.000 39 0 0 1 39 29988576 29988614 3.960000e-09 73.1
5 TraesCS2D01G065000 chr2B 92.870 2202 88 22 160 2311 44157997 44160179 0.000000e+00 3133.0
6 TraesCS2D01G065000 chr2B 92.079 505 33 4 2362 2864 44160192 44160691 0.000000e+00 704.0
7 TraesCS2D01G065000 chr4B 80.323 620 111 11 1229 1844 547093972 547094584 2.600000e-125 459.0
8 TraesCS2D01G065000 chr1B 80.118 508 78 15 1230 1727 264763400 264763894 9.760000e-95 357.0
9 TraesCS2D01G065000 chr3D 78.333 540 102 14 1230 1763 157443377 157442847 4.570000e-88 335.0
10 TraesCS2D01G065000 chr3A 78.044 542 103 14 1230 1763 170811690 170812223 7.650000e-86 327.0
11 TraesCS2D01G065000 chr3B 77.473 546 108 14 1230 1769 228690784 228690248 2.140000e-81 313.0
12 TraesCS2D01G065000 chr3B 100.000 52 0 0 2309 2360 649519671 649519722 2.350000e-16 97.1
13 TraesCS2D01G065000 chr3B 98.077 52 1 0 2309 2360 156702348 156702399 1.090000e-14 91.6
14 TraesCS2D01G065000 chr7D 84.444 315 46 2 1231 1542 501116276 501116590 9.970000e-80 307.0
15 TraesCS2D01G065000 chr1D 77.362 508 92 15 1230 1727 191374481 191374975 2.170000e-71 279.0
16 TraesCS2D01G065000 chr1D 94.545 55 1 2 2308 2360 487320438 487320492 1.830000e-12 84.2
17 TraesCS2D01G065000 chr5B 77.753 445 82 13 1114 1551 619927318 619926884 1.020000e-64 257.0
18 TraesCS2D01G065000 chr5B 77.581 339 54 20 1225 1550 662036914 662036585 4.870000e-43 185.0
19 TraesCS2D01G065000 chr5A 77.455 448 82 17 1114 1551 623504413 623503975 1.700000e-62 250.0
20 TraesCS2D01G065000 chr5A 95.556 45 2 0 1114 1158 653717283 653717239 3.960000e-09 73.1
21 TraesCS2D01G065000 chr6A 98.148 54 1 0 2307 2360 223535840 223535893 8.450000e-16 95.3
22 TraesCS2D01G065000 chr6A 96.226 53 2 0 2308 2360 826938 826886 1.410000e-13 87.9
23 TraesCS2D01G065000 chr6B 98.113 53 1 0 2308 2360 162172833 162172781 3.040000e-15 93.5
24 TraesCS2D01G065000 chr4A 98.113 53 1 0 2308 2360 507582273 507582221 3.040000e-15 93.5
25 TraesCS2D01G065000 chrUn 96.226 53 1 1 2308 2360 23410132 23410081 5.080000e-13 86.1
26 TraesCS2D01G065000 chrUn 96.226 53 1 1 2308 2360 302105993 302105942 5.080000e-13 86.1
27 TraesCS2D01G065000 chr5D 95.652 46 2 0 1115 1160 499246703 499246658 1.100000e-09 75.0
28 TraesCS2D01G065000 chr5D 93.617 47 3 0 1114 1160 526572237 526572191 1.420000e-08 71.3


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 TraesCS2D01G065000 chr2D 27835822 27838685 2863 False 5289.000000 5289 100.0000 1 2864 1 chr2D.!!$F1 2863
1 TraesCS2D01G065000 chr2A 29988576 29991332 2756 False 1364.366667 3336 96.0340 1 2807 3 chr2A.!!$F2 2806
2 TraesCS2D01G065000 chr2B 44157997 44160691 2694 False 1918.500000 3133 92.4745 160 2864 2 chr2B.!!$F1 2704
3 TraesCS2D01G065000 chr4B 547093972 547094584 612 False 459.000000 459 80.3230 1229 1844 1 chr4B.!!$F1 615
4 TraesCS2D01G065000 chr3D 157442847 157443377 530 True 335.000000 335 78.3330 1230 1763 1 chr3D.!!$R1 533
5 TraesCS2D01G065000 chr3A 170811690 170812223 533 False 327.000000 327 78.0440 1230 1763 1 chr3A.!!$F1 533
6 TraesCS2D01G065000 chr3B 228690248 228690784 536 True 313.000000 313 77.4730 1230 1769 1 chr3B.!!$R1 539

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
267 275 0.038159 CCTCGGTCGCTTTCAAGAGT 60.038 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2219 1.139498 TTCTGGCCAATGGGAGGACA 61.139 55.0 7.01 0.0 43.42 4.02 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
56 57 4.790962 CAGCACATCGCCAGCCCT 62.791 66.667 0.00 0.00 44.04 5.19
59 60 4.864334 CACATCGCCAGCCCTCCC 62.864 72.222 0.00 0.00 0.00 4.30
66 67 4.351054 CCAGCCCTCCCACACCAC 62.351 72.222 0.00 0.00 0.00 4.16
67 68 3.569210 CAGCCCTCCCACACCACA 61.569 66.667 0.00 0.00 0.00 4.17
68 69 2.776526 AGCCCTCCCACACCACAA 60.777 61.111 0.00 0.00 0.00 3.33
69 70 2.282462 GCCCTCCCACACCACAAG 60.282 66.667 0.00 0.00 0.00 3.16
70 71 2.282462 CCCTCCCACACCACAAGC 60.282 66.667 0.00 0.00 0.00 4.01
71 72 2.515398 CCTCCCACACCACAAGCA 59.485 61.111 0.00 0.00 0.00 3.91
72 73 1.075482 CCTCCCACACCACAAGCAT 59.925 57.895 0.00 0.00 0.00 3.79
73 74 1.246056 CCTCCCACACCACAAGCATG 61.246 60.000 0.00 0.00 0.00 4.06
74 75 1.228521 TCCCACACCACAAGCATGG 60.229 57.895 0.00 0.00 46.10 3.66
75 76 2.652530 CCACACCACAAGCATGGC 59.347 61.111 0.00 0.00 44.33 4.40
76 77 2.652530 CACACCACAAGCATGGCC 59.347 61.111 0.00 0.00 44.33 5.36
77 78 2.601367 ACACCACAAGCATGGCCC 60.601 61.111 0.00 0.00 44.33 5.80
78 79 2.601067 CACCACAAGCATGGCCCA 60.601 61.111 0.00 0.00 44.33 5.36
79 80 2.601367 ACCACAAGCATGGCCCAC 60.601 61.111 0.00 0.00 44.33 4.61
80 81 3.384532 CCACAAGCATGGCCCACC 61.385 66.667 0.00 0.00 31.52 4.61
81 82 2.283388 CACAAGCATGGCCCACCT 60.283 61.111 0.00 0.00 36.63 4.00
82 83 2.036256 ACAAGCATGGCCCACCTC 59.964 61.111 0.00 0.00 36.63 3.85
83 84 3.136123 CAAGCATGGCCCACCTCG 61.136 66.667 0.00 0.00 36.63 4.63
84 85 3.650950 AAGCATGGCCCACCTCGT 61.651 61.111 0.00 0.00 36.63 4.18
185 188 2.261671 CGTCGCCAGCACCTACTT 59.738 61.111 0.00 0.00 0.00 2.24
267 275 0.038159 CCTCGGTCGCTTTCAAGAGT 60.038 55.000 0.00 0.00 0.00 3.24
314 322 2.304470 TCACCGGATGTTGGATCTTTGA 59.696 45.455 9.46 0.00 0.00 2.69
321 329 4.511826 GGATGTTGGATCTTTGACGATACC 59.488 45.833 0.00 0.00 0.00 2.73
336 344 2.673833 GATACCGAGCCCTTCAATACG 58.326 52.381 0.00 0.00 0.00 3.06
368 376 0.734889 AAGCGCCATCATTTCTTCGG 59.265 50.000 2.29 0.00 0.00 4.30
406 414 4.715297 ACTCAGTGAACCCGGACTATATTT 59.285 41.667 0.73 0.00 0.00 1.40
489 498 4.499037 GAAACACTTTCCCCATGTGTAC 57.501 45.455 0.00 0.00 41.73 2.90
490 499 2.579410 ACACTTTCCCCATGTGTACC 57.421 50.000 0.00 0.00 40.99 3.34
491 500 1.074889 ACACTTTCCCCATGTGTACCC 59.925 52.381 0.00 0.00 40.99 3.69
492 501 1.074727 CACTTTCCCCATGTGTACCCA 59.925 52.381 0.00 0.00 0.00 4.51
493 502 1.354368 ACTTTCCCCATGTGTACCCAG 59.646 52.381 0.00 0.00 0.00 4.45
494 503 1.354368 CTTTCCCCATGTGTACCCAGT 59.646 52.381 0.00 0.00 0.00 4.00
511 520 0.696501 AGTACCCACGGCCAAAAGAT 59.303 50.000 2.24 0.00 0.00 2.40
543 552 2.113774 TGTGCAGCACAGGGGAAG 59.886 61.111 24.84 0.00 39.62 3.46
544 553 2.431683 GTGCAGCACAGGGGAAGA 59.568 61.111 21.22 0.00 34.08 2.87
606 616 1.583404 CAGATGCAAATTAAACGCCGC 59.417 47.619 0.00 0.00 0.00 6.53
607 617 1.201181 AGATGCAAATTAAACGCCGCA 59.799 42.857 0.00 0.00 0.00 5.69
608 618 2.159254 AGATGCAAATTAAACGCCGCAT 60.159 40.909 0.00 0.00 42.45 4.73
609 619 1.623359 TGCAAATTAAACGCCGCATC 58.377 45.000 0.00 0.00 0.00 3.91
610 620 0.920664 GCAAATTAAACGCCGCATCC 59.079 50.000 0.00 0.00 0.00 3.51
611 621 1.555477 CAAATTAAACGCCGCATCCC 58.445 50.000 0.00 0.00 0.00 3.85
612 622 0.099791 AAATTAAACGCCGCATCCCG 59.900 50.000 0.00 0.00 0.00 5.14
882 905 3.184683 GCCAGCAGAGCTTCGTCG 61.185 66.667 0.00 0.00 36.40 5.12
956 980 3.230134 ACTCCTAGATCTGCCTGTCATC 58.770 50.000 5.18 0.00 0.00 2.92
970 994 1.075970 TCATCTCCGGCCACTAGCT 60.076 57.895 2.24 0.00 43.05 3.32
1004 1028 5.505324 GCTTCATTGATCTCTGTAACATGGC 60.505 44.000 0.00 0.00 0.00 4.40
1184 1211 5.411781 CGCAGGAGTAGTTAACTTCATTCT 58.588 41.667 14.49 1.53 39.07 2.40
1198 1225 7.905604 AACTTCATTCTATCGTGATGAACAA 57.094 32.000 0.00 0.00 0.00 2.83
1677 1713 1.447838 CGTGTCCATCAAGGGGTCG 60.448 63.158 0.00 0.00 38.24 4.79
1742 1778 3.782244 GTCCAACGCGCTGCTCAG 61.782 66.667 5.73 0.00 0.00 3.35
2147 2215 3.536158 TCTGAAAAGGAAAATGACGCG 57.464 42.857 3.53 3.53 0.00 6.01
2151 2219 3.181495 TGAAAAGGAAAATGACGCGTGTT 60.181 39.130 20.70 8.84 0.00 3.32
2159 2227 2.737376 GACGCGTGTTGTCCTCCC 60.737 66.667 20.70 0.00 0.00 4.30
2307 2393 7.830099 AAAGGTTTGATGAGAAATGAAGAGT 57.170 32.000 0.00 0.00 0.00 3.24
2311 2397 8.699130 AGGTTTGATGAGAAATGAAGAGTTTTT 58.301 29.630 0.00 0.00 0.00 1.94
2332 2418 1.995376 TTTGAAAAGGAGGTCAGCCC 58.005 50.000 0.00 0.00 34.57 5.19
2333 2419 0.112412 TTGAAAAGGAGGTCAGCCCC 59.888 55.000 0.00 0.00 34.57 5.80
2334 2420 1.000771 GAAAAGGAGGTCAGCCCCC 60.001 63.158 0.00 0.00 34.57 5.40
2335 2421 2.821679 GAAAAGGAGGTCAGCCCCCG 62.822 65.000 0.00 0.00 34.57 5.73
2350 2436 3.933722 CCGGCCTCTGCATCGGAT 61.934 66.667 0.00 0.00 42.71 4.18
2351 2437 2.574018 CCGGCCTCTGCATCGGATA 61.574 63.158 0.00 0.00 42.71 2.59
2352 2438 1.080230 CGGCCTCTGCATCGGATAG 60.080 63.158 0.00 0.00 40.13 2.08
2353 2439 1.527433 CGGCCTCTGCATCGGATAGA 61.527 60.000 0.00 0.00 40.13 1.98
2354 2440 0.901124 GGCCTCTGCATCGGATAGAT 59.099 55.000 0.00 0.00 41.01 1.98
2437 2523 4.620589 ACAATGCAAACATGGGATTCAA 57.379 36.364 0.00 0.00 36.36 2.69
2453 2539 6.379703 TGGGATTCAATACCACTGTTAATTGG 59.620 38.462 0.00 0.39 38.72 3.16
2481 2567 3.863142 ATTTGTCTTGCCAGCAGATTC 57.137 42.857 0.00 0.00 0.00 2.52
2490 2576 3.159472 TGCCAGCAGATTCACTTCAATT 58.841 40.909 0.00 0.00 0.00 2.32
2566 2652 2.437651 TGATCCGGACTATCCAATTGCA 59.562 45.455 6.12 0.00 35.91 4.08
2587 2673 5.221891 CACAGTATGCTGGTGAAATGTAC 57.778 43.478 15.65 0.00 46.62 2.90
2615 2701 7.963361 TGGTTATGCCGGATATTGATTCTCAAT 60.963 37.037 5.05 7.45 44.02 2.57
2631 2717 1.824230 TCAATTTCCGGCCCTGAAATG 59.176 47.619 22.13 17.05 40.57 2.32
2773 2865 5.450818 TGGGTAAGATGCCTTTCACTTAT 57.549 39.130 0.00 0.00 33.94 1.73
2816 2909 2.252012 TAGGCCCAAGATCCCGGACT 62.252 60.000 0.73 4.23 38.96 3.85
2819 2912 0.544697 GCCCAAGATCCCGGACTTAA 59.455 55.000 0.73 0.00 0.00 1.85
2822 2915 2.172717 CCCAAGATCCCGGACTTAATGT 59.827 50.000 0.73 0.00 0.00 2.71
2832 2925 3.061322 CGGACTTAATGTCGTTGGTTGA 58.939 45.455 0.00 0.00 46.24 3.18
2852 2945 6.264067 GGTTGATAGAATGGAAAGGAGATTGG 59.736 42.308 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.790962 AGGGCTGGCGATGTGCTG 62.791 66.667 0.00 0.00 45.43 4.41
40 41 4.479993 GAGGGCTGGCGATGTGCT 62.480 66.667 0.00 0.00 45.43 4.40
42 43 4.864334 GGGAGGGCTGGCGATGTG 62.864 72.222 0.00 0.00 0.00 3.21
44 45 4.864334 GTGGGAGGGCTGGCGATG 62.864 72.222 0.00 0.00 0.00 3.84
49 50 4.351054 GTGGTGTGGGAGGGCTGG 62.351 72.222 0.00 0.00 0.00 4.85
50 51 3.132029 TTGTGGTGTGGGAGGGCTG 62.132 63.158 0.00 0.00 0.00 4.85
51 52 2.776526 TTGTGGTGTGGGAGGGCT 60.777 61.111 0.00 0.00 0.00 5.19
55 56 1.246056 CCATGCTTGTGGTGTGGGAG 61.246 60.000 0.00 0.00 34.46 4.30
56 57 1.228521 CCATGCTTGTGGTGTGGGA 60.229 57.895 0.00 0.00 34.46 4.37
58 59 2.652530 GCCATGCTTGTGGTGTGG 59.347 61.111 0.00 0.00 41.47 4.17
59 60 2.652530 GGCCATGCTTGTGGTGTG 59.347 61.111 0.00 0.00 41.47 3.82
60 61 2.601367 GGGCCATGCTTGTGGTGT 60.601 61.111 4.39 0.00 41.47 4.16
62 63 2.601367 GTGGGCCATGCTTGTGGT 60.601 61.111 10.70 0.00 41.47 4.16
63 64 3.384532 GGTGGGCCATGCTTGTGG 61.385 66.667 10.70 0.00 42.35 4.17
64 65 2.283388 AGGTGGGCCATGCTTGTG 60.283 61.111 10.70 0.00 37.19 3.33
65 66 2.036256 GAGGTGGGCCATGCTTGT 59.964 61.111 10.70 0.00 37.19 3.16
66 67 3.136123 CGAGGTGGGCCATGCTTG 61.136 66.667 10.70 0.00 37.19 4.01
67 68 3.628646 GACGAGGTGGGCCATGCTT 62.629 63.158 10.70 0.00 37.19 3.91
68 69 4.101448 GACGAGGTGGGCCATGCT 62.101 66.667 10.70 0.00 37.19 3.79
77 78 4.436998 GACCAGGGCGACGAGGTG 62.437 72.222 8.12 0.00 38.16 4.00
80 81 4.135153 CTGGACCAGGGCGACGAG 62.135 72.222 14.26 0.00 0.00 4.18
133 134 2.202756 CCTAGCGCGGTGGAGTTC 60.203 66.667 23.80 0.00 0.00 3.01
147 148 0.254154 TGGGGTCCTCTCTCTCCCTA 60.254 60.000 0.00 0.00 39.80 3.53
267 275 2.221299 CCCCCTTTCCCTCGTGTCA 61.221 63.158 0.00 0.00 0.00 3.58
314 322 1.120530 ATTGAAGGGCTCGGTATCGT 58.879 50.000 0.00 0.00 37.69 3.73
321 329 0.174845 TGTCCGTATTGAAGGGCTCG 59.825 55.000 0.00 0.00 32.36 5.03
336 344 0.388520 GGCGCTTTGTTTGGATGTCC 60.389 55.000 7.64 0.00 0.00 4.02
368 376 7.360776 GGTTCACTGAGTTCAAGATCAAATCTC 60.361 40.741 0.00 0.00 39.08 2.75
406 414 4.046286 ACAAACAAGATGCCCAGGAATA 57.954 40.909 0.00 0.00 0.00 1.75
488 497 4.966274 TGGCCGTGGGTACTGGGT 62.966 66.667 0.00 0.00 0.00 4.51
489 498 2.700407 TTTTGGCCGTGGGTACTGGG 62.700 60.000 0.00 0.00 0.00 4.45
490 499 1.228306 TTTTGGCCGTGGGTACTGG 60.228 57.895 0.00 0.00 0.00 4.00
491 500 0.250553 TCTTTTGGCCGTGGGTACTG 60.251 55.000 0.00 0.00 0.00 2.74
492 501 0.696501 ATCTTTTGGCCGTGGGTACT 59.303 50.000 0.00 0.00 0.00 2.73
493 502 0.808755 CATCTTTTGGCCGTGGGTAC 59.191 55.000 0.00 0.00 0.00 3.34
494 503 0.963355 GCATCTTTTGGCCGTGGGTA 60.963 55.000 0.00 0.00 0.00 3.69
511 520 1.573932 CACAGTCAAATTCGGCGCA 59.426 52.632 10.83 0.00 0.00 6.09
540 549 1.715993 GGGCTTCGTGTCTTCTCTTC 58.284 55.000 0.00 0.00 0.00 2.87
541 550 0.038159 CGGGCTTCGTGTCTTCTCTT 60.038 55.000 0.00 0.00 0.00 2.85
542 551 1.587054 CGGGCTTCGTGTCTTCTCT 59.413 57.895 0.00 0.00 0.00 3.10
543 552 1.446272 CCGGGCTTCGTGTCTTCTC 60.446 63.158 0.00 0.00 37.11 2.87
544 553 1.258445 ATCCGGGCTTCGTGTCTTCT 61.258 55.000 0.00 0.00 37.11 2.85
606 616 1.592400 GGATGGATGCATGCGGGATG 61.592 60.000 14.09 4.99 34.84 3.51
607 617 1.303888 GGATGGATGCATGCGGGAT 60.304 57.895 14.09 0.05 0.00 3.85
608 618 2.113774 GGATGGATGCATGCGGGA 59.886 61.111 14.09 0.00 0.00 5.14
609 619 2.203379 TGGATGGATGCATGCGGG 60.203 61.111 14.09 0.00 0.00 6.13
610 620 2.916052 GCTGGATGGATGCATGCGG 61.916 63.158 20.98 20.98 33.20 5.69
611 621 2.643272 GCTGGATGGATGCATGCG 59.357 61.111 14.09 9.62 0.00 4.73
612 622 1.524863 GAGGCTGGATGGATGCATGC 61.525 60.000 11.82 11.82 0.00 4.06
910 934 4.789075 GCCATGCCTTGCACTGCG 62.789 66.667 0.00 0.00 43.04 5.18
956 980 0.889306 GGTATAGCTAGTGGCCGGAG 59.111 60.000 5.05 0.00 43.05 4.63
970 994 6.988580 CAGAGATCAATGAAGCTTGTGGTATA 59.011 38.462 2.10 0.00 0.00 1.47
1004 1028 1.583967 GACGATCCAGCTGACGTCG 60.584 63.158 29.13 26.71 43.60 5.12
1184 1211 6.220201 TCTTTCTGTGTTGTTCATCACGATA 58.780 36.000 0.00 5.11 37.38 2.92
1198 1225 3.439476 GCATCATCAGCTTCTTTCTGTGT 59.561 43.478 0.00 0.00 33.48 3.72
1239 1272 3.698820 AGGTTCCCGTACCCGCAC 61.699 66.667 0.00 0.00 39.08 5.34
1677 1713 4.176752 GGCATCCACCCCGTCCTC 62.177 72.222 0.00 0.00 0.00 3.71
2147 2215 1.250840 GGCCAATGGGAGGACAACAC 61.251 60.000 0.00 0.00 35.59 3.32
2151 2219 1.139498 TTCTGGCCAATGGGAGGACA 61.139 55.000 7.01 0.00 43.42 4.02
2159 2227 4.796038 AGAAATTCAGTTCTGGCCAATG 57.204 40.909 7.01 3.56 36.48 2.82
2212 2297 1.818060 TCTCAAAATCCACCAATGCCG 59.182 47.619 0.00 0.00 0.00 5.69
2255 2340 7.839907 ACTTTAAAATTTGCAGGATAGCATCA 58.160 30.769 0.00 0.00 45.19 3.07
2311 2397 2.698274 GGGCTGACCTCCTTTTCAAAAA 59.302 45.455 0.00 0.00 35.85 1.94
2312 2398 2.316108 GGGCTGACCTCCTTTTCAAAA 58.684 47.619 0.00 0.00 35.85 2.44
2313 2399 1.480498 GGGGCTGACCTCCTTTTCAAA 60.480 52.381 0.00 0.00 40.03 2.69
2315 2401 1.767692 GGGGCTGACCTCCTTTTCA 59.232 57.895 0.00 0.00 40.03 2.69
2316 2402 4.745116 GGGGCTGACCTCCTTTTC 57.255 61.111 0.00 0.00 40.03 2.29
2333 2419 2.498291 CTATCCGATGCAGAGGCCGG 62.498 65.000 0.00 0.00 43.53 6.13
2334 2420 1.080230 CTATCCGATGCAGAGGCCG 60.080 63.158 0.00 0.00 40.13 6.13
2335 2421 0.901124 ATCTATCCGATGCAGAGGCC 59.099 55.000 0.00 0.00 40.13 5.19
2336 2422 2.007360 CATCTATCCGATGCAGAGGC 57.993 55.000 5.43 0.00 42.75 4.70
2344 2430 5.163364 GGATAAGACCATGCATCTATCCGAT 60.163 44.000 0.00 0.00 0.00 4.18
2345 2431 4.160439 GGATAAGACCATGCATCTATCCGA 59.840 45.833 0.00 0.00 0.00 4.55
2346 2432 4.161189 AGGATAAGACCATGCATCTATCCG 59.839 45.833 15.68 0.00 34.67 4.18
2347 2433 5.424895 AGAGGATAAGACCATGCATCTATCC 59.575 44.000 14.69 14.69 32.32 2.59
2348 2434 6.543430 AGAGGATAAGACCATGCATCTATC 57.457 41.667 0.00 0.00 0.00 2.08
2349 2435 5.126869 CGAGAGGATAAGACCATGCATCTAT 59.873 44.000 0.00 0.00 0.00 1.98
2350 2436 4.460731 CGAGAGGATAAGACCATGCATCTA 59.539 45.833 0.00 0.00 0.00 1.98
2351 2437 3.257873 CGAGAGGATAAGACCATGCATCT 59.742 47.826 0.00 0.00 0.00 2.90
2352 2438 3.256879 TCGAGAGGATAAGACCATGCATC 59.743 47.826 0.00 0.00 0.00 3.91
2353 2439 3.234353 TCGAGAGGATAAGACCATGCAT 58.766 45.455 0.00 0.00 0.00 3.96
2354 2440 2.666317 TCGAGAGGATAAGACCATGCA 58.334 47.619 0.00 0.00 0.00 3.96
2355 2441 3.181475 TGTTCGAGAGGATAAGACCATGC 60.181 47.826 0.00 0.00 0.00 4.06
2356 2442 4.363999 GTGTTCGAGAGGATAAGACCATG 58.636 47.826 0.00 0.00 0.00 3.66
2357 2443 3.385111 GGTGTTCGAGAGGATAAGACCAT 59.615 47.826 0.00 0.00 36.74 3.55
2358 2444 2.758979 GGTGTTCGAGAGGATAAGACCA 59.241 50.000 0.00 0.00 36.74 4.02
2359 2445 3.025262 AGGTGTTCGAGAGGATAAGACC 58.975 50.000 0.00 0.00 36.94 3.85
2360 2446 4.440387 GGAAGGTGTTCGAGAGGATAAGAC 60.440 50.000 0.00 0.00 32.92 3.01
2414 2500 5.327616 TGAATCCCATGTTTGCATTGTAG 57.672 39.130 0.00 0.00 31.99 2.74
2437 2523 5.570320 AGAAGTGCCAATTAACAGTGGTAT 58.430 37.500 0.00 0.00 40.57 2.73
2453 2539 3.671702 GCTGGCAAGACAAATAGAAGTGC 60.672 47.826 0.00 0.00 0.00 4.40
2481 2567 5.989249 TGTCATCGAGAACAAATTGAAGTG 58.011 37.500 0.00 0.00 0.00 3.16
2490 2576 6.873605 ACAAAGATACATGTCATCGAGAACAA 59.126 34.615 0.00 0.00 0.00 2.83
2566 2652 5.165961 AGTACATTTCACCAGCATACTGT 57.834 39.130 0.00 0.00 42.81 3.55
2577 2663 4.438200 CCGGCATAACCAAGTACATTTCAC 60.438 45.833 0.00 0.00 39.03 3.18
2581 2667 3.637911 TCCGGCATAACCAAGTACATT 57.362 42.857 0.00 0.00 39.03 2.71
2586 2672 4.431416 TCAATATCCGGCATAACCAAGT 57.569 40.909 0.00 0.00 39.03 3.16
2587 2673 5.707298 AGAATCAATATCCGGCATAACCAAG 59.293 40.000 0.00 0.00 39.03 3.61
2615 2701 1.824230 CATTCATTTCAGGGCCGGAAA 59.176 47.619 29.45 29.45 38.49 3.13
2773 2865 2.299867 GTGTACCCTGGGTAAACGAAGA 59.700 50.000 26.45 3.69 40.12 2.87
2816 2909 7.106890 TCCATTCTATCAACCAACGACATTAA 58.893 34.615 0.00 0.00 0.00 1.40
2819 2912 5.097742 TCCATTCTATCAACCAACGACAT 57.902 39.130 0.00 0.00 0.00 3.06
2822 2915 4.941263 CCTTTCCATTCTATCAACCAACGA 59.059 41.667 0.00 0.00 0.00 3.85
2832 2925 6.331307 AGCTACCAATCTCCTTTCCATTCTAT 59.669 38.462 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.