Multiple sequence alignment - TraesCS5D01G150600

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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 TraesCS5D01G150600 chr5D 100.000 6605 0 0 1 6605 239587032 239580428 0.000000e+00 12198.0
1 TraesCS5D01G150600 chr5D 78.475 223 41 4 457 678 441884452 441884668 8.930000e-29 139.0
2 TraesCS5D01G150600 chr5D 85.897 78 4 3 3165 3235 519637230 519637153 7.100000e-10 76.8
3 TraesCS5D01G150600 chr5D 90.476 42 4 0 2770 2811 415270276 415270317 1.000000e-03 56.5
4 TraesCS5D01G150600 chr5B 95.352 4927 134 26 769 5646 263934380 263939260 0.000000e+00 7742.0
5 TraesCS5D01G150600 chr5B 86.375 800 63 21 1 789 263780734 263781498 0.000000e+00 832.0
6 TraesCS5D01G150600 chr5B 90.260 154 13 2 3230 3382 645807622 645807470 4.040000e-47 200.0
7 TraesCS5D01G150600 chr5B 97.059 34 0 1 3481 3513 654481948 654481915 1.000000e-03 56.5
8 TraesCS5D01G150600 chr5B 90.698 43 3 1 720 761 671085230 671085272 1.000000e-03 56.5
9 TraesCS5D01G150600 chr5A 96.731 1560 43 4 3492 5044 314145814 314147372 0.000000e+00 2591.0
10 TraesCS5D01G150600 chr5A 91.829 1689 80 25 1 1668 314142503 314144154 0.000000e+00 2302.0
11 TraesCS5D01G150600 chr5A 90.774 1745 76 37 1703 3445 314144152 314145813 0.000000e+00 2252.0
12 TraesCS5D01G150600 chr5A 91.347 1618 70 28 5030 6604 314148649 314150239 0.000000e+00 2148.0
13 TraesCS5D01G150600 chr5A 89.677 155 15 1 3230 3383 502803729 502803575 5.230000e-46 196.0
14 TraesCS5D01G150600 chr7A 81.791 670 99 12 1596 2262 527977711 527978360 2.100000e-149 540.0
15 TraesCS5D01G150600 chr7A 78.531 177 35 3 421 595 642591190 642591365 5.410000e-21 113.0
16 TraesCS5D01G150600 chr1B 80.316 569 73 23 6036 6578 14261195 14261750 1.730000e-105 394.0
17 TraesCS5D01G150600 chr1B 82.245 383 60 5 1632 2013 684220673 684221048 2.300000e-84 324.0
18 TraesCS5D01G150600 chr1B 92.857 42 2 1 721 761 536120718 536120677 7.150000e-05 60.2
19 TraesCS5D01G150600 chr6D 80.508 472 66 16 6144 6596 373390969 373390505 8.200000e-89 339.0
20 TraesCS5D01G150600 chr6D 78.229 542 69 33 6071 6577 346562666 346563193 1.080000e-77 302.0
21 TraesCS5D01G150600 chr6D 77.143 385 52 27 6218 6577 437348213 437347840 2.430000e-44 191.0
22 TraesCS5D01G150600 chr6D 78.361 305 46 12 6039 6336 393643386 393643677 5.260000e-41 180.0
23 TraesCS5D01G150600 chr6D 90.323 62 5 1 2753 2813 464967313 464967252 5.490000e-11 80.5
24 TraesCS5D01G150600 chr6D 89.583 48 5 0 5785 5832 455296041 455296088 1.990000e-05 62.1
25 TraesCS5D01G150600 chr1D 79.618 471 68 18 6094 6546 447223427 447223887 4.970000e-81 313.0
26 TraesCS5D01G150600 chr1D 95.349 43 2 0 2770 2812 378722260 378722218 1.190000e-07 69.4
27 TraesCS5D01G150600 chr1A 83.333 312 52 0 1638 1949 589674683 589674372 8.380000e-74 289.0
28 TraesCS5D01G150600 chr1A 95.349 43 2 0 2770 2812 578209373 578209415 1.190000e-07 69.4
29 TraesCS5D01G150600 chr3D 88.384 198 18 1 1757 1949 604254961 604255158 3.980000e-57 233.0
30 TraesCS5D01G150600 chr3D 90.476 63 5 1 3452 3513 378197507 378197445 1.530000e-11 82.4
31 TraesCS5D01G150600 chr4D 90.968 155 12 2 3229 3382 329540574 329540421 2.410000e-49 207.0
32 TraesCS5D01G150600 chr4D 86.154 65 5 2 2771 2831 471966299 471966235 4.270000e-07 67.6
33 TraesCS5D01G150600 chr7B 90.323 155 14 1 3229 3382 329936619 329936465 1.120000e-47 202.0
34 TraesCS5D01G150600 chr7B 78.599 257 42 10 294 543 449542450 449542700 2.470000e-34 158.0
35 TraesCS5D01G150600 chr7B 97.778 45 0 1 136 180 594698954 594698997 7.100000e-10 76.8
36 TraesCS5D01G150600 chr7B 86.885 61 7 1 119 179 504480717 504480776 4.270000e-07 67.6
37 TraesCS5D01G150600 chr6B 89.610 154 15 1 3230 3382 150881055 150880902 1.880000e-45 195.0
38 TraesCS5D01G150600 chr6B 89.610 154 15 1 3230 3382 356597454 356597607 1.880000e-45 195.0
39 TraesCS5D01G150600 chr6B 95.652 46 2 0 134 179 632997846 632997801 2.550000e-09 75.0
40 TraesCS5D01G150600 chr6B 95.122 41 2 0 2770 2810 719740140 719740100 1.540000e-06 65.8
41 TraesCS5D01G150600 chr6B 86.792 53 5 2 3467 3517 8413782 8413834 2.570000e-04 58.4
42 TraesCS5D01G150600 chr6B 85.965 57 1 5 723 778 142132172 142132122 3.000000e-03 54.7
43 TraesCS5D01G150600 chr4A 85.246 183 21 4 3273 3449 242899435 242899617 4.070000e-42 183.0
44 TraesCS5D01G150600 chr4A 79.141 163 32 2 421 581 625256555 625256393 1.950000e-20 111.0
45 TraesCS5D01G150600 chr6A 76.623 385 54 18 6218 6577 585582695 585582322 5.260000e-41 180.0
46 TraesCS5D01G150600 chr6A 92.500 40 2 1 723 761 442400408 442400369 1.000000e-03 56.5
47 TraesCS5D01G150600 chr2B 75.253 396 75 17 294 678 109056989 109057372 4.100000e-37 167.0
48 TraesCS5D01G150600 chr2B 78.182 220 35 11 456 670 647744598 647744387 1.930000e-25 128.0
49 TraesCS5D01G150600 chr2B 94.444 54 1 1 134 185 190922284 190922231 1.530000e-11 82.4
50 TraesCS5D01G150600 chr7D 76.923 286 53 11 296 571 138494615 138494897 4.130000e-32 150.0
51 TraesCS5D01G150600 chr2D 91.071 56 3 2 134 188 439396420 439396474 2.550000e-09 75.0
52 TraesCS5D01G150600 chr2D 86.275 51 7 0 5782 5832 461804157 461804207 1.000000e-03 56.5
53 TraesCS5D01G150600 chr4B 95.556 45 2 0 136 180 454694213 454694169 9.190000e-09 73.1
54 TraesCS5D01G150600 chr4B 92.500 40 2 1 723 761 28183141 28183102 1.000000e-03 56.5
55 TraesCS5D01G150600 chr4B 92.500 40 2 1 723 761 28187222 28187183 1.000000e-03 56.5
56 TraesCS5D01G150600 chr4B 92.500 40 2 1 723 761 664908643 664908604 1.000000e-03 56.5
57 TraesCS5D01G150600 chr3A 88.333 60 5 2 120 179 642283923 642283866 3.300000e-08 71.3
58 TraesCS5D01G150600 chr3A 90.909 44 4 0 2770 2813 516549985 516550028 7.150000e-05 60.2
59 TraesCS5D01G150600 chr3A 100.000 32 0 0 5801 5832 727180264 727180233 7.150000e-05 60.2
60 TraesCS5D01G150600 chrUn 94.872 39 2 0 723 761 20829119 20829081 1.990000e-05 62.1


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 TraesCS5D01G150600 chr5D 239580428 239587032 6604 True 12198.00 12198 100.00000 1 6605 1 chr5D.!!$R1 6604
1 TraesCS5D01G150600 chr5B 263934380 263939260 4880 False 7742.00 7742 95.35200 769 5646 1 chr5B.!!$F2 4877
2 TraesCS5D01G150600 chr5B 263780734 263781498 764 False 832.00 832 86.37500 1 789 1 chr5B.!!$F1 788
3 TraesCS5D01G150600 chr5A 314142503 314150239 7736 False 2323.25 2591 92.67025 1 6604 4 chr5A.!!$F1 6603
4 TraesCS5D01G150600 chr7A 527977711 527978360 649 False 540.00 540 81.79100 1596 2262 1 chr7A.!!$F1 666
5 TraesCS5D01G150600 chr1B 14261195 14261750 555 False 394.00 394 80.31600 6036 6578 1 chr1B.!!$F1 542
6 TraesCS5D01G150600 chr6D 346562666 346563193 527 False 302.00 302 78.22900 6071 6577 1 chr6D.!!$F1 506

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
134 138 0.400670 ATAGCTCTTGACCCTCCCCC 60.401 60.000 0.00 0.00 0.00 5.40 F
515 532 0.676466 TTAGGGGCACGTGCATGAAG 60.676 55.000 38.60 5.84 44.36 3.02 F
2006 2079 0.038166 AAACTGGCCACGGTCATCAT 59.962 50.000 0.00 0.00 34.35 2.45 F
3013 3109 0.802607 GTCACCGGCGTCAGAGAATC 60.803 60.000 6.01 0.00 0.00 2.52 F
3518 3616 0.755327 AAAGCTGAACAAACGGGGCT 60.755 50.000 0.00 0.00 0.00 5.19 F
4497 4599 2.095461 TCACTCGAGGAACCTCATCAG 58.905 52.381 18.41 13.43 42.86 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1859 0.389948 GAGGAGGTTGCAACGATCGT 60.390 55.000 22.67 21.94 0.00 3.73 R
2153 2233 1.000163 TGCTATCAAGGCGCTAGCTAC 60.000 52.381 21.60 5.24 44.37 3.58 R
3325 3422 0.112412 ACTGAAAATGGCCCGAACCT 59.888 50.000 0.00 0.00 0.00 3.50 R
4509 4611 0.468226 TGCTCTTTCGTGGGACAGTT 59.532 50.000 0.00 0.00 41.80 3.16 R
5239 6636 1.032014 CACTGGGTTTGGTTGTCAGG 58.968 55.000 0.00 0.00 0.00 3.86 R
5970 7394 0.374758 CGCACTGCATCGCTTACATT 59.625 50.000 1.11 0.00 0.00 2.71 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 1.561542 GAAGGGAGGAATTGGAGAGCA 59.438 52.381 0.00 0.00 0.00 4.26
62 63 4.894114 GGGCTACTACAAGGTGATCTAGAA 59.106 45.833 0.00 0.00 0.00 2.10
63 64 5.540719 GGGCTACTACAAGGTGATCTAGAAT 59.459 44.000 0.00 0.00 0.00 2.40
64 65 6.042208 GGGCTACTACAAGGTGATCTAGAATT 59.958 42.308 0.00 0.00 0.00 2.17
80 84 9.877178 GATCTAGAATTCTTCTTCAGTGGTTTA 57.123 33.333 14.36 0.00 41.14 2.01
116 120 0.970427 GGCGGGTGGTGGATTTGAAT 60.970 55.000 0.00 0.00 0.00 2.57
134 138 0.400670 ATAGCTCTTGACCCTCCCCC 60.401 60.000 0.00 0.00 0.00 5.40
179 183 6.685828 CACACTCATGCATATTCGAGAAAAAG 59.314 38.462 16.34 5.55 0.00 2.27
242 248 4.787135 TGGAATCATGCCCAATGTAGTA 57.213 40.909 0.00 0.00 37.56 1.82
302 309 1.865248 GCATGCAACACACGCTTCTTT 60.865 47.619 14.21 0.00 0.00 2.52
304 311 1.378531 TGCAACACACGCTTCTTTCT 58.621 45.000 0.00 0.00 0.00 2.52
318 325 5.453587 CGCTTCTTTCTTGAGTTTGTCTTTG 59.546 40.000 0.00 0.00 0.00 2.77
322 329 3.662759 TCTTGAGTTTGTCTTTGGGGT 57.337 42.857 0.00 0.00 0.00 4.95
323 330 3.551846 TCTTGAGTTTGTCTTTGGGGTC 58.448 45.455 0.00 0.00 0.00 4.46
324 331 3.202151 TCTTGAGTTTGTCTTTGGGGTCT 59.798 43.478 0.00 0.00 0.00 3.85
336 344 1.075896 GGGGTCTGATCCTCCTCGT 60.076 63.158 6.95 0.00 0.00 4.18
343 351 2.632996 TCTGATCCTCCTCGTGTTTGTT 59.367 45.455 0.00 0.00 0.00 2.83
371 379 1.300971 CGTAGTCGACAGGGTTCCGA 61.301 60.000 19.50 0.00 39.71 4.55
381 389 1.201429 AGGGTTCCGACATTCCTGCT 61.201 55.000 0.00 0.00 0.00 4.24
438 447 2.299013 TGTGGCGAGATTTAGTGTCAGT 59.701 45.455 0.00 0.00 0.00 3.41
443 452 3.061429 GCGAGATTTAGTGTCAGTTGCTC 59.939 47.826 0.00 0.00 0.00 4.26
450 459 1.277557 AGTGTCAGTTGCTCCAGATCC 59.722 52.381 0.00 0.00 0.00 3.36
510 527 1.302192 GTTCTTAGGGGCACGTGCA 60.302 57.895 38.60 18.47 44.36 4.57
515 532 0.676466 TTAGGGGCACGTGCATGAAG 60.676 55.000 38.60 5.84 44.36 3.02
529 546 5.618395 CGTGCATGAAGATTTATCGATTGTG 59.382 40.000 1.71 0.00 0.00 3.33
571 588 4.752879 GTAGGGCAGCGGCGACAA 62.753 66.667 12.98 0.00 42.47 3.18
572 589 4.752879 TAGGGCAGCGGCGACAAC 62.753 66.667 12.98 0.00 42.47 3.32
671 691 8.716619 TTATGTTTGACACGCTTTGTATTTAC 57.283 30.769 0.00 0.00 39.17 2.01
682 702 6.128117 ACGCTTTGTATTTACGGTGAAATCAT 60.128 34.615 0.00 0.00 31.51 2.45
719 739 6.484643 TGATCCTTTGAAAAGAGAGACACTTG 59.515 38.462 4.34 0.00 38.28 3.16
971 999 2.356673 GCAGCAAGCCAAGCCAAC 60.357 61.111 0.00 0.00 37.23 3.77
980 1008 2.576832 CCAAGCCAACCCAAGCCAG 61.577 63.158 0.00 0.00 0.00 4.85
1024 1052 1.012486 GTCGTCGGCGTTCAAATCCT 61.012 55.000 10.18 0.00 39.49 3.24
1559 1587 8.990163 TTGGAAAAGAACAGATAAGGTTAAGT 57.010 30.769 0.00 0.00 0.00 2.24
1561 1589 9.498176 TGGAAAAGAACAGATAAGGTTAAGTAC 57.502 33.333 0.00 0.00 0.00 2.73
1786 1859 7.175467 AGTCACAAATCAACTGATTGCATTCTA 59.825 33.333 5.72 0.00 43.41 2.10
2006 2079 0.038166 AAACTGGCCACGGTCATCAT 59.962 50.000 0.00 0.00 34.35 2.45
2157 2237 9.921637 AGATGAAGCTCTAATATAGTTTGTAGC 57.078 33.333 0.00 0.00 0.00 3.58
2426 2507 5.979517 TGTCAGATTGCTGTATTATCTGTCG 59.020 40.000 10.17 0.00 43.56 4.35
2470 2551 1.075542 CGTGTTAGCTTGGCGATTCA 58.924 50.000 0.00 0.00 0.00 2.57
2619 2700 3.618690 ATGTGAGTTGCCCTTCTACTC 57.381 47.619 0.00 0.00 44.34 2.59
2637 2718 6.494952 TCTACTCTGGACCTTAGATTGAACT 58.505 40.000 0.00 0.00 0.00 3.01
2661 2742 8.632679 ACTGTTTTTGTACATGACATCTTCAAT 58.367 29.630 0.00 0.00 37.92 2.57
2763 2844 0.878961 GAGTACCGGGGCGCTTATTG 60.879 60.000 7.64 0.00 0.00 1.90
2802 2883 2.295349 TGCGGAAGAAGTCGACTTAGTT 59.705 45.455 29.79 24.29 36.11 2.24
3013 3109 0.802607 GTCACCGGCGTCAGAGAATC 60.803 60.000 6.01 0.00 0.00 2.52
3023 3119 4.094212 GCGTCAGAGAATCAAAGAATTGC 58.906 43.478 0.00 0.00 37.82 3.56
3024 3120 4.378770 GCGTCAGAGAATCAAAGAATTGCA 60.379 41.667 0.00 0.00 37.82 4.08
3025 3121 5.322310 CGTCAGAGAATCAAAGAATTGCAG 58.678 41.667 0.00 0.00 37.82 4.41
3026 3122 5.106791 CGTCAGAGAATCAAAGAATTGCAGT 60.107 40.000 0.00 0.00 37.82 4.40
3325 3422 0.901827 TGCCGGTGAAGCTGAATCTA 59.098 50.000 1.90 0.00 0.00 1.98
3404 3501 1.336240 GCTTTGCCAGTGAAGCGAATT 60.336 47.619 0.00 0.00 38.89 2.17
3455 3552 6.389906 GTTAAACAAACAGGCTGCATAATCT 58.610 36.000 15.89 0.00 38.05 2.40
3456 3553 4.445452 AACAAACAGGCTGCATAATCTG 57.555 40.909 15.89 1.40 0.00 2.90
3518 3616 0.755327 AAAGCTGAACAAACGGGGCT 60.755 50.000 0.00 0.00 0.00 5.19
3607 3707 7.667219 AGAAGAACATAACATGGAGTTCACATT 59.333 33.333 17.84 8.48 42.01 2.71
3676 3778 5.523916 TCTTCTTCTAAGTTGTTCACTGTGC 59.476 40.000 2.12 0.00 35.12 4.57
3835 3937 5.765182 ACAGAATTCAAACGGAGAGATGTTT 59.235 36.000 8.44 0.00 38.76 2.83
4054 4156 4.440802 GGTCTTCAGTTCTATGCTGTCGAT 60.441 45.833 0.00 0.00 35.60 3.59
4497 4599 2.095461 TCACTCGAGGAACCTCATCAG 58.905 52.381 18.41 13.43 42.86 2.90
4509 4611 3.184628 ACCTCATCAGAATTCAGGTGGA 58.815 45.455 12.37 1.05 36.06 4.02
4682 4784 6.778108 TCAAGTTTCTTTTCTTACAACGACC 58.222 36.000 0.00 0.00 0.00 4.79
4833 4935 8.621532 TGGTGCAGAATATCTATTAACCATTC 57.378 34.615 0.00 0.00 0.00 2.67
4844 4946 8.773033 ATCTATTAACCATTCCTGAAAATGCT 57.227 30.769 0.00 0.00 35.68 3.79
4906 5008 6.302313 CGTTTGAAATAAAACTGTAGAAGCGG 59.698 38.462 0.00 0.00 37.80 5.52
5299 6696 5.336770 GGATCTGATGTGTCTGACAGTGTTA 60.337 44.000 11.41 0.00 38.23 2.41
5431 6837 4.994217 TGAAAGCTGTCGACAATTGTGATA 59.006 37.500 20.49 10.85 0.00 2.15
5477 6883 4.329528 CAGCAGAGTAATCAGCAAAGAGAC 59.670 45.833 10.25 0.00 0.00 3.36
5720 7141 1.701704 CTTTTGTTGATTGCGCCTCC 58.298 50.000 4.18 0.00 0.00 4.30
5736 7157 4.731612 CCGCAGCGACACAGAGCT 62.732 66.667 18.75 0.00 45.74 4.09
5751 7173 7.900352 CGACACAGAGCTGTATTTTTCTAATTC 59.100 37.037 2.36 0.00 42.83 2.17
5847 7269 7.330262 TCATATCTAAGTTGTGACATCAGCAA 58.670 34.615 0.00 0.00 0.00 3.91
5859 7281 1.267806 CATCAGCAAAAGTCAGCGGTT 59.732 47.619 0.00 0.00 35.48 4.44
5889 7311 5.213675 CCCGCGTTGTCTTATTTTTGTTTA 58.786 37.500 4.92 0.00 0.00 2.01
5930 7352 3.110178 CCCACCGCGTCGTTCTTC 61.110 66.667 4.92 0.00 0.00 2.87
5931 7353 2.049433 CCACCGCGTCGTTCTTCT 60.049 61.111 4.92 0.00 0.00 2.85
5932 7354 2.087009 CCACCGCGTCGTTCTTCTC 61.087 63.158 4.92 0.00 0.00 2.87
5940 7364 3.660777 GCGTCGTTCTTCTCTTATTTGC 58.339 45.455 0.00 0.00 0.00 3.68
5960 7384 2.657237 CTTTCCCGACTGGAGCGT 59.343 61.111 0.00 0.00 46.24 5.07
5966 7390 0.882927 CCCGACTGGAGCGTGAAAAA 60.883 55.000 0.00 0.00 37.49 1.94
5998 7422 1.926510 CGATGCAGTGCGTTGAATAGA 59.073 47.619 18.38 0.00 31.01 1.98
6015 7439 5.874810 TGAATAGAAATTGAACTCAGGACCG 59.125 40.000 0.00 0.00 0.00 4.79
6016 7440 5.677319 ATAGAAATTGAACTCAGGACCGA 57.323 39.130 0.00 0.00 0.00 4.69
6017 7441 4.559862 AGAAATTGAACTCAGGACCGAT 57.440 40.909 0.00 0.00 0.00 4.18
6019 7443 6.049955 AGAAATTGAACTCAGGACCGATAA 57.950 37.500 0.00 0.00 0.00 1.75
6030 7482 3.189287 CAGGACCGATAAATGCTATTGCC 59.811 47.826 0.00 0.00 38.71 4.52
6061 7513 4.813296 ACAGGAAACGTTCAAGAACATC 57.187 40.909 12.86 7.53 41.20 3.06
6099 7558 3.721035 AGGCACACTTGAAGATTTTTGC 58.279 40.909 0.00 0.00 0.00 3.68
6259 7726 7.812669 AGAACAAAATTTGGTATTCCGATCAAC 59.187 33.333 10.71 0.00 36.30 3.18
6268 7735 5.186992 TGGTATTCCGATCAACTTCTTCTCA 59.813 40.000 0.00 0.00 36.30 3.27
6439 7932 7.095229 GGTTTGCTCCCTTTAAAAATGTTCATC 60.095 37.037 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.905357 CACCTTGTAGTAGCCCAGCT 59.095 55.000 0.00 0.00 43.41 4.24
62 63 6.013293 ACCTAGCTAAACCACTGAAGAAGAAT 60.013 38.462 0.00 0.00 0.00 2.40
63 64 5.307196 ACCTAGCTAAACCACTGAAGAAGAA 59.693 40.000 0.00 0.00 0.00 2.52
64 65 4.838986 ACCTAGCTAAACCACTGAAGAAGA 59.161 41.667 0.00 0.00 0.00 2.87
80 84 1.221840 CCGCAACATCCACCTAGCT 59.778 57.895 0.00 0.00 0.00 3.32
116 120 1.003051 GGGGGAGGGTCAAGAGCTA 59.997 63.158 0.00 0.00 0.00 3.32
179 183 9.758651 AAAACCTCAACAGTAATGGATTTAAAC 57.241 29.630 0.00 0.00 0.00 2.01
289 295 2.906354 ACTCAAGAAAGAAGCGTGTGT 58.094 42.857 0.00 0.00 0.00 3.72
290 296 3.951979 AACTCAAGAAAGAAGCGTGTG 57.048 42.857 0.00 0.00 0.00 3.82
291 297 3.689649 ACAAACTCAAGAAAGAAGCGTGT 59.310 39.130 0.00 0.00 0.00 4.49
295 301 5.745769 CCAAAGACAAACTCAAGAAAGAAGC 59.254 40.000 0.00 0.00 0.00 3.86
302 309 3.202151 AGACCCCAAAGACAAACTCAAGA 59.798 43.478 0.00 0.00 0.00 3.02
304 311 3.053991 TCAGACCCCAAAGACAAACTCAA 60.054 43.478 0.00 0.00 0.00 3.02
318 325 1.075896 ACGAGGAGGATCAGACCCC 60.076 63.158 0.00 0.00 36.25 4.95
322 329 2.248248 ACAAACACGAGGAGGATCAGA 58.752 47.619 0.00 0.00 36.25 3.27
323 330 2.751166 ACAAACACGAGGAGGATCAG 57.249 50.000 0.00 0.00 36.25 2.90
324 331 2.609491 CGAACAAACACGAGGAGGATCA 60.609 50.000 0.00 0.00 36.25 2.92
366 374 3.532896 GACAGCAGGAATGTCGGAA 57.467 52.632 0.00 0.00 37.88 4.30
371 379 1.004044 CCAAGGAGACAGCAGGAATGT 59.996 52.381 0.00 0.00 0.00 2.71
372 380 1.681166 CCCAAGGAGACAGCAGGAATG 60.681 57.143 0.00 0.00 0.00 2.67
373 381 0.622665 CCCAAGGAGACAGCAGGAAT 59.377 55.000 0.00 0.00 0.00 3.01
381 389 3.636231 CACCGCCCCAAGGAGACA 61.636 66.667 0.00 0.00 34.21 3.41
430 439 1.277557 GGATCTGGAGCAACTGACACT 59.722 52.381 0.00 0.00 0.00 3.55
438 447 1.683938 CCTTGCATGGATCTGGAGCAA 60.684 52.381 13.33 12.34 42.27 3.91
443 452 1.341285 TGAACCCTTGCATGGATCTGG 60.341 52.381 19.85 5.34 0.00 3.86
450 459 0.948623 TCGTCGTGAACCCTTGCATG 60.949 55.000 0.00 0.00 0.00 4.06
488 498 1.125711 ACGTGCCCCTAAGAACCAGT 61.126 55.000 0.00 0.00 0.00 4.00
510 527 9.112725 TGTCAATCACAATCGATAAATCTTCAT 57.887 29.630 0.00 0.00 29.30 2.57
515 532 7.697691 ACCTTGTCAATCACAATCGATAAATC 58.302 34.615 0.00 0.00 44.32 2.17
588 606 2.813754 CGATCACCACTGTCACCAAAAT 59.186 45.455 0.00 0.00 0.00 1.82
706 726 7.445945 ACTTTATACTTGCAAGTGTCTCTCTT 58.554 34.615 36.50 13.26 40.07 2.85
967 995 4.619320 TGGCCTGGCTTGGGTTGG 62.619 66.667 19.68 0.00 0.00 3.77
968 996 2.993264 CTGGCCTGGCTTGGGTTG 60.993 66.667 19.68 0.00 0.00 3.77
969 997 4.305956 CCTGGCCTGGCTTGGGTT 62.306 66.667 19.68 0.00 0.00 4.11
1189 1217 2.443016 CGGAGGTGGAGAGGAGGG 60.443 72.222 0.00 0.00 0.00 4.30
1221 1249 1.690985 CTTCCTCCCTCTGTCCCCC 60.691 68.421 0.00 0.00 0.00 5.40
1533 1561 9.588096 ACTTAACCTTATCTGTTCTTTTCCAAT 57.412 29.630 0.00 0.00 0.00 3.16
1680 1746 1.139853 GCTGGCCACTCTTATAGCACT 59.860 52.381 0.00 0.00 0.00 4.40
1786 1859 0.389948 GAGGAGGTTGCAACGATCGT 60.390 55.000 22.67 21.94 0.00 3.73
2006 2079 2.054021 TGCTATAGGGGCTATTGCACA 58.946 47.619 3.26 0.00 44.99 4.57
2153 2233 1.000163 TGCTATCAAGGCGCTAGCTAC 60.000 52.381 21.60 5.24 44.37 3.58
2426 2507 6.648725 GGCATAAACATTCCTAGACTCATCTC 59.351 42.308 0.00 0.00 36.29 2.75
2470 2551 9.965902 AAGAACAGAATCCTTCATTAGTAACAT 57.034 29.630 0.00 0.00 0.00 2.71
2619 2700 6.884280 AAAACAGTTCAATCTAAGGTCCAG 57.116 37.500 0.00 0.00 0.00 3.86
2661 2742 3.136809 TGAAGTTTGGTACCAAGGCACTA 59.863 43.478 25.74 11.03 38.49 2.74
2729 2810 3.198863 GTACTCAGGTACAGTGACACG 57.801 52.381 0.00 0.00 45.41 4.49
2802 2883 7.915293 CATTACAATGGACTAAACACCTACA 57.085 36.000 0.00 0.00 32.78 2.74
2899 2995 4.764679 TGATGCACACAACAATCCTTAC 57.235 40.909 0.00 0.00 0.00 2.34
3013 3109 7.526608 TCCGTATAAAAGACTGCAATTCTTTG 58.473 34.615 18.96 9.44 41.48 2.77
3023 3119 7.117236 TGTGCTAACTTTCCGTATAAAAGACTG 59.883 37.037 2.84 0.00 37.22 3.51
3024 3120 7.156673 TGTGCTAACTTTCCGTATAAAAGACT 58.843 34.615 2.84 0.00 37.22 3.24
3025 3121 7.355332 TGTGCTAACTTTCCGTATAAAAGAC 57.645 36.000 2.84 0.00 37.22 3.01
3026 3122 8.556213 AATGTGCTAACTTTCCGTATAAAAGA 57.444 30.769 2.84 0.00 37.22 2.52
3325 3422 0.112412 ACTGAAAATGGCCCGAACCT 59.888 50.000 0.00 0.00 0.00 3.50
3404 3501 5.184711 TGATTGGATTCGAATCACATGTGA 58.815 37.500 32.92 29.67 44.59 3.58
3455 3552 1.098869 TTCGCTTCACTGGCAAAACA 58.901 45.000 0.00 0.00 0.00 2.83
3456 3553 2.319472 GATTCGCTTCACTGGCAAAAC 58.681 47.619 0.00 0.00 0.00 2.43
3607 3707 7.566760 ACGCATTTGGTCAATAAATATCTGA 57.433 32.000 0.00 0.00 0.00 3.27
3676 3778 8.345565 GGCCTATTGATGAAACAGTAACAATAG 58.654 37.037 1.54 1.54 42.67 1.73
3835 3937 6.209391 GGATCAAACTCAAGAGGAATTTCCAA 59.791 38.462 17.57 0.00 39.61 3.53
4174 4276 2.993937 TCGGACAAACTTGGAACAGTT 58.006 42.857 0.00 0.00 42.39 3.16
4497 4599 2.224769 TGGGACAGTTCCACCTGAATTC 60.225 50.000 0.00 0.00 44.98 2.17
4509 4611 0.468226 TGCTCTTTCGTGGGACAGTT 59.532 50.000 0.00 0.00 41.80 3.16
4682 4784 9.355215 CAGTCTTAATAAAGTGTACTACCACTG 57.645 37.037 0.00 0.00 44.74 3.66
4833 4935 7.046652 TCTCTCTATTTCTCAGCATTTTCAGG 58.953 38.462 0.00 0.00 0.00 3.86
5239 6636 1.032014 CACTGGGTTTGGTTGTCAGG 58.968 55.000 0.00 0.00 0.00 3.86
5299 6696 3.372025 GGGGACTTGGCATGACTAAAGAT 60.372 47.826 5.67 0.00 0.00 2.40
5431 6837 7.439655 GCTGAAACTCCTTAGATATTGACGAAT 59.560 37.037 0.00 0.00 0.00 3.34
5477 6883 4.028383 GTCATCGGCACAATAATTTGACG 58.972 43.478 0.00 0.00 36.64 4.35
5699 7120 0.388659 AGGCGCAATCAACAAAAGCA 59.611 45.000 10.83 0.00 0.00 3.91
5701 7122 1.701704 GGAGGCGCAATCAACAAAAG 58.298 50.000 10.83 0.00 0.00 2.27
5720 7141 3.476646 CAGCTCTGTGTCGCTGCG 61.477 66.667 17.25 17.25 45.90 5.18
5777 7199 9.593134 GATGCTATATAGTCAGACCCAAAATAG 57.407 37.037 11.38 0.19 0.00 1.73
5820 7242 7.147846 TGCTGATGTCACAACTTAGATATGAGA 60.148 37.037 0.00 0.00 0.00 3.27
5821 7243 6.982724 TGCTGATGTCACAACTTAGATATGAG 59.017 38.462 0.00 0.00 0.00 2.90
5825 7247 7.661437 ACTTTTGCTGATGTCACAACTTAGATA 59.339 33.333 0.00 0.00 0.00 1.98
5832 7254 4.285292 CTGACTTTTGCTGATGTCACAAC 58.715 43.478 0.00 0.00 35.83 3.32
5847 7269 0.663153 GCTGAACAACCGCTGACTTT 59.337 50.000 0.00 0.00 0.00 2.66
5859 7281 2.933878 AAGACAACGCGGGCTGAACA 62.934 55.000 12.47 0.00 0.00 3.18
5928 7350 3.440173 CGGGAAAGCAGCAAATAAGAGAA 59.560 43.478 0.00 0.00 0.00 2.87
5930 7352 3.009723 TCGGGAAAGCAGCAAATAAGAG 58.990 45.455 0.00 0.00 0.00 2.85
5931 7353 2.747446 GTCGGGAAAGCAGCAAATAAGA 59.253 45.455 0.00 0.00 0.00 2.10
5932 7354 2.749621 AGTCGGGAAAGCAGCAAATAAG 59.250 45.455 0.00 0.00 0.00 1.73
5970 7394 0.374758 CGCACTGCATCGCTTACATT 59.625 50.000 1.11 0.00 0.00 2.71
5971 7395 0.740868 ACGCACTGCATCGCTTACAT 60.741 50.000 1.11 0.00 0.00 2.29
5987 7411 6.024049 CCTGAGTTCAATTTCTATTCAACGC 58.976 40.000 0.00 0.00 30.89 4.84
5998 7422 6.404734 GCATTTATCGGTCCTGAGTTCAATTT 60.405 38.462 0.00 0.00 0.00 1.82
6015 7439 4.037446 TCCCAAACGGCAATAGCATTTATC 59.963 41.667 0.00 0.00 44.61 1.75
6016 7440 3.957497 TCCCAAACGGCAATAGCATTTAT 59.043 39.130 0.00 0.00 44.61 1.40
6017 7441 3.357203 TCCCAAACGGCAATAGCATTTA 58.643 40.909 0.00 0.00 44.61 1.40
6019 7443 1.846007 TCCCAAACGGCAATAGCATT 58.154 45.000 0.00 0.00 44.61 3.56
6030 7482 2.113910 CGTTTCCTGTTTCCCAAACG 57.886 50.000 1.83 1.83 44.28 3.60
6061 7513 0.810031 CCTTGTAATCTGGACCCGCG 60.810 60.000 0.00 0.00 0.00 6.46
6287 7754 4.211920 TCGGGGATTTTCAAAAGTTGTCT 58.788 39.130 0.00 0.00 0.00 3.41
6293 7761 4.584327 ACTGTTCGGGGATTTTCAAAAG 57.416 40.909 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.