Multiple sequence alignment - TraesCS4A01G206200

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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 TraesCS4A01G206200 chr4A 100.000 5402 0 0 1 5402 499340534 499345935 0.000000e+00 9976.0
1 TraesCS4A01G206200 chr4D 96.820 4969 106 23 160 5115 85578374 85583303 0.000000e+00 8253.0
2 TraesCS4A01G206200 chr4D 89.583 144 9 2 5123 5266 85583367 85583504 1.550000e-40 178.0
3 TraesCS4A01G206200 chr4B 92.690 3037 126 40 2137 5124 122521623 122524612 0.000000e+00 4290.0
4 TraesCS4A01G206200 chr4B 92.727 2145 94 31 1 2104 122519505 122521628 0.000000e+00 3040.0
5 TraesCS4A01G206200 chr4B 85.517 290 25 10 5122 5402 122524666 122524947 2.460000e-73 287.0
6 TraesCS4A01G206200 chr5D 90.441 544 48 2 1067 1606 177684261 177683718 0.000000e+00 713.0
7 TraesCS4A01G206200 chr5D 92.593 135 8 2 2842 2974 177681823 177681689 5.520000e-45 193.0
8 TraesCS4A01G206200 chr5D 80.460 87 17 0 2876 2962 184874224 184874310 3.490000e-07 67.6
9 TraesCS4A01G206200 chr5A 90.441 544 48 2 1067 1606 191036298 191036841 0.000000e+00 713.0
10 TraesCS4A01G206200 chr5A 92.593 135 8 2 2842 2974 191038747 191038881 5.520000e-45 193.0
11 TraesCS4A01G206200 chr5B 90.257 544 49 2 1067 1606 192383290 192382747 0.000000e+00 708.0
12 TraesCS4A01G206200 chr5B 91.852 135 9 2 2842 2974 192380892 192380758 2.570000e-43 187.0
13 TraesCS4A01G206200 chr2D 80.040 496 85 11 1118 1606 564095494 564095006 6.650000e-94 355.0
14 TraesCS4A01G206200 chr2B 80.000 495 87 9 1118 1606 675356180 675355692 6.650000e-94 355.0
15 TraesCS4A01G206200 chr2A 79.435 496 88 11 1118 1606 704776749 704776261 6.700000e-89 339.0
16 TraesCS4A01G206200 chr6B 79.744 390 65 12 1154 1536 717076808 717076426 2.480000e-68 270.0
17 TraesCS4A01G206200 chr6B 75.833 480 104 11 1133 1606 519720425 519720898 3.250000e-57 233.0
18 TraesCS4A01G206200 chr6D 76.042 480 103 11 1133 1606 344207897 344208370 6.990000e-59 239.0


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 TraesCS4A01G206200 chr4A 499340534 499345935 5401 False 9976.0 9976 100.000000 1 5402 1 chr4A.!!$F1 5401
1 TraesCS4A01G206200 chr4D 85578374 85583504 5130 False 4215.5 8253 93.201500 160 5266 2 chr4D.!!$F1 5106
2 TraesCS4A01G206200 chr4B 122519505 122524947 5442 False 2539.0 4290 90.311333 1 5402 3 chr4B.!!$F1 5401
3 TraesCS4A01G206200 chr5D 177681689 177684261 2572 True 453.0 713 91.517000 1067 2974 2 chr5D.!!$R1 1907
4 TraesCS4A01G206200 chr5A 191036298 191038881 2583 False 453.0 713 91.517000 1067 2974 2 chr5A.!!$F1 1907
5 TraesCS4A01G206200 chr5B 192380758 192383290 2532 True 447.5 708 91.054500 1067 2974 2 chr5B.!!$R1 1907

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
599 639 0.189574 TTGTGCCAATCTTTCCCCCA 59.810 50.000 0.0 0.0 0.00 4.96 F
615 655 1.279271 CCCCAGTTCTTCCGTTCTCAT 59.721 52.381 0.0 0.0 0.00 2.90 F
744 784 3.691609 CCATAAAGCTCCTTTTTCTCGCT 59.308 43.478 0.0 0.0 35.21 4.93 F
1691 1743 0.040067 CCAGTTCGAGCTTTGTTGGC 60.040 55.000 0.0 0.0 0.00 4.52 F
3253 4134 0.826715 TCTCTGGCTACCATCAGTGC 59.173 55.000 0.0 0.0 30.82 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1559 0.608640 GGAAGTTCTCCGGCTTGAGA 59.391 55.000 0.0 0.0 39.58 3.27 R
1560 1607 1.200020 CCAAAATCGGTGGTCTTGAGC 59.800 52.381 0.0 0.0 0.00 4.26 R
2067 2239 2.550830 ATGAACGCACTTGTCTTCCT 57.449 45.000 0.0 0.0 0.00 3.36 R
3514 4398 3.372025 GCCATAAACCCTCAAGACTCCAT 60.372 47.826 0.0 0.0 0.00 3.41 R
5244 6213 0.793250 GCGTGGAAGCTCTCTGTTTC 59.207 55.000 0.0 0.0 35.52 2.78 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
27 28 2.668144 AAGGGGAAACAACCGATTCA 57.332 45.000 0.00 0.00 0.00 2.57
31 32 1.957877 GGGAAACAACCGATTCAACCA 59.042 47.619 0.00 0.00 0.00 3.67
34 35 4.234574 GGAAACAACCGATTCAACCATTC 58.765 43.478 0.00 0.00 0.00 2.67
41 42 1.810151 CGATTCAACCATTCCCAACGT 59.190 47.619 0.00 0.00 0.00 3.99
44 45 1.313772 TCAACCATTCCCAACGTGTG 58.686 50.000 0.00 0.00 0.00 3.82
48 49 1.285641 CATTCCCAACGTGTGTGGC 59.714 57.895 0.00 0.00 0.00 5.01
50 51 1.172180 ATTCCCAACGTGTGTGGCTG 61.172 55.000 0.00 0.00 0.00 4.85
60 61 0.616111 TGTGTGGCTGGGGTTTGTTT 60.616 50.000 0.00 0.00 0.00 2.83
69 70 3.133183 GCTGGGGTTTGTTTTAAGGTTCA 59.867 43.478 0.00 0.00 0.00 3.18
76 77 7.386573 GGGGTTTGTTTTAAGGTTCATGTTATG 59.613 37.037 0.00 0.00 0.00 1.90
77 78 7.929245 GGGTTTGTTTTAAGGTTCATGTTATGT 59.071 33.333 0.00 0.00 0.00 2.29
93 95 5.739959 TGTTATGTAGGCAAGCAGTGAATA 58.260 37.500 0.00 0.00 0.00 1.75
96 98 4.220693 TGTAGGCAAGCAGTGAATACAT 57.779 40.909 0.00 0.00 29.56 2.29
97 99 5.351948 TGTAGGCAAGCAGTGAATACATA 57.648 39.130 0.00 0.00 29.56 2.29
100 102 5.614324 AGGCAAGCAGTGAATACATACTA 57.386 39.130 0.00 0.00 0.00 1.82
102 104 6.595682 AGGCAAGCAGTGAATACATACTATT 58.404 36.000 0.00 0.00 0.00 1.73
110 112 7.440255 GCAGTGAATACATACTATTAAACGGGT 59.560 37.037 0.00 0.00 0.00 5.28
120 133 6.334102 ACTATTAAACGGGTCATTTTTGCA 57.666 33.333 0.00 0.00 0.00 4.08
123 136 3.467374 AAACGGGTCATTTTTGCATGT 57.533 38.095 0.00 0.00 0.00 3.21
125 138 3.467374 ACGGGTCATTTTTGCATGTTT 57.533 38.095 0.00 0.00 0.00 2.83
136 149 1.294138 GCATGTTTGGGCTGCATGT 59.706 52.632 0.50 0.00 41.27 3.21
137 150 0.531657 GCATGTTTGGGCTGCATGTA 59.468 50.000 0.50 0.00 41.27 2.29
147 160 4.324471 TGCATGTAGGCAGCCAAG 57.676 55.556 15.80 0.00 39.25 3.61
151 164 1.746615 ATGTAGGCAGCCAAGCACG 60.747 57.895 15.80 0.00 35.83 5.34
152 165 2.358737 GTAGGCAGCCAAGCACGT 60.359 61.111 15.80 0.00 35.83 4.49
158 171 1.639298 GCAGCCAAGCACGTCCTTAG 61.639 60.000 0.00 0.00 0.00 2.18
214 233 6.374053 TCCGATAATGAATGTTTTGCTGAGAA 59.626 34.615 0.00 0.00 0.00 2.87
217 236 8.581263 CGATAATGAATGTTTTGCTGAGAAAAG 58.419 33.333 0.00 0.00 0.00 2.27
302 323 1.057851 TCCTGAAAACCCCGTGGAGT 61.058 55.000 0.00 0.00 34.81 3.85
303 324 0.605589 CCTGAAAACCCCGTGGAGTC 60.606 60.000 0.00 0.00 34.81 3.36
304 325 0.949105 CTGAAAACCCCGTGGAGTCG 60.949 60.000 0.00 0.00 34.81 4.18
305 326 1.070275 GAAAACCCCGTGGAGTCGT 59.930 57.895 0.00 0.00 34.81 4.34
306 327 1.226030 GAAAACCCCGTGGAGTCGTG 61.226 60.000 0.00 0.00 34.81 4.35
308 329 4.928140 ACCCCGTGGAGTCGTGGT 62.928 66.667 0.00 0.00 36.82 4.16
309 330 2.677524 CCCCGTGGAGTCGTGGTA 60.678 66.667 0.00 0.00 0.00 3.25
310 331 2.570181 CCCGTGGAGTCGTGGTAC 59.430 66.667 0.00 0.00 0.00 3.34
311 332 2.177531 CCGTGGAGTCGTGGTACG 59.822 66.667 0.00 0.00 44.19 3.67
339 360 0.251916 TGACCTAACAATCCTGCCCG 59.748 55.000 0.00 0.00 0.00 6.13
340 361 0.463833 GACCTAACAATCCTGCCCGG 60.464 60.000 0.00 0.00 0.00 5.73
341 362 1.823899 CCTAACAATCCTGCCCGGC 60.824 63.158 1.04 1.04 0.00 6.13
342 363 1.077787 CTAACAATCCTGCCCGGCA 60.078 57.895 12.67 12.67 36.92 5.69
445 481 4.547905 CCATCGTCCCCGTCGTCG 62.548 72.222 0.00 0.00 35.01 5.12
594 634 4.590850 AAGAGGTTTGTGCCAATCTTTC 57.409 40.909 0.00 0.00 0.00 2.62
599 639 0.189574 TTGTGCCAATCTTTCCCCCA 59.810 50.000 0.00 0.00 0.00 4.96
615 655 1.279271 CCCCAGTTCTTCCGTTCTCAT 59.721 52.381 0.00 0.00 0.00 2.90
744 784 3.691609 CCATAAAGCTCCTTTTTCTCGCT 59.308 43.478 0.00 0.00 35.21 4.93
1655 1707 8.559536 ACATGTGTAGTACTTTGTTCTTTCATG 58.440 33.333 0.00 6.58 34.58 3.07
1691 1743 0.040067 CCAGTTCGAGCTTTGTTGGC 60.040 55.000 0.00 0.00 0.00 4.52
1915 2021 6.998074 CCTAGTATTAATGAATGTCAAGGGCA 59.002 38.462 0.00 0.00 0.00 5.36
2005 2111 5.758790 AGATATGATGGCTGCAAGATACT 57.241 39.130 0.50 0.00 34.07 2.12
2067 2239 5.842328 ACTATTTCGGAACCTCATATGGGTA 59.158 40.000 14.09 1.51 35.83 3.69
2080 2252 2.789409 ATGGGTAGGAAGACAAGTGC 57.211 50.000 0.00 0.00 0.00 4.40
2322 2686 8.568732 TTACTTAAAATTTTCTGTTTGAGCCG 57.431 30.769 6.72 0.00 0.00 5.52
2757 3574 3.844211 TGTAAGTGCACCTCCTCCTTATT 59.156 43.478 14.63 0.00 0.00 1.40
2768 3585 5.367060 ACCTCCTCCTTATTACTCATGGAAC 59.633 44.000 0.00 0.00 0.00 3.62
3025 3879 6.119536 TCTTTTTGAGCAGAAAACTGTAGGA 58.880 36.000 0.00 0.00 0.00 2.94
3027 3881 6.767524 TTTTGAGCAGAAAACTGTAGGAAA 57.232 33.333 0.00 0.00 0.00 3.13
3253 4134 0.826715 TCTCTGGCTACCATCAGTGC 59.173 55.000 0.00 0.00 30.82 4.40
3469 4353 2.878406 CAATGCTGTTATTAGGTCCCCG 59.122 50.000 0.00 0.00 0.00 5.73
3799 4687 1.553690 GGGTGGGCTCAGAGCTAACA 61.554 60.000 21.99 15.16 41.99 2.41
3860 4748 5.731263 GCTTCGTTACAAGCTAAATAAACGG 59.269 40.000 15.24 6.07 44.71 4.44
3982 4871 8.137437 GGAACGATTGATTATGGTGAATTCATT 58.863 33.333 12.12 2.76 0.00 2.57
4182 5071 8.902540 AACAATGTCAGTGTTTCTTCATACTA 57.097 30.769 12.70 0.00 35.70 1.82
4183 5072 8.902540 ACAATGTCAGTGTTTCTTCATACTAA 57.097 30.769 0.00 0.00 0.00 2.24
4188 5077 8.999431 TGTCAGTGTTTCTTCATACTAAATTCC 58.001 33.333 0.00 0.00 0.00 3.01
4199 5088 2.354328 ACTAAATTCCACCCTGTCCCA 58.646 47.619 0.00 0.00 0.00 4.37
4311 5200 0.179100 AGTTCACGGCGATGATGAGG 60.179 55.000 16.62 0.00 0.00 3.86
4450 5339 4.310642 CCTGGTGGATGCCATTTTGTGG 62.311 54.545 0.00 0.00 43.04 4.17
4483 5372 2.311463 GCCTGATCAGCTGGACTACTA 58.689 52.381 17.76 0.00 37.79 1.82
4484 5373 2.035321 GCCTGATCAGCTGGACTACTAC 59.965 54.545 17.76 0.00 37.79 2.73
4485 5374 3.561143 CCTGATCAGCTGGACTACTACT 58.439 50.000 17.76 0.00 37.79 2.57
4671 5561 1.322538 GCCGGGGATTGCATCAACTT 61.323 55.000 2.18 0.00 0.00 2.66
4823 5713 7.491696 AGTGACGAGGTAGTATAAAATTTCTGC 59.508 37.037 0.00 0.00 0.00 4.26
4866 5757 5.988092 ACAATTTTGCACAAATTGAATCCG 58.012 33.333 31.33 17.33 45.59 4.18
4921 5813 9.480861 AACTGCACTATCTATCTATAGGCATAA 57.519 33.333 0.00 0.00 36.22 1.90
4922 5814 9.653516 ACTGCACTATCTATCTATAGGCATAAT 57.346 33.333 0.00 0.00 36.22 1.28
4923 5815 9.911138 CTGCACTATCTATCTATAGGCATAATG 57.089 37.037 0.00 0.00 36.22 1.90
4924 5816 8.363390 TGCACTATCTATCTATAGGCATAATGC 58.637 37.037 0.00 4.33 44.08 3.56
4936 5829 2.159057 GGCATAATGCTTTGTCCTTGGG 60.159 50.000 0.00 0.00 44.28 4.12
4940 5833 1.632589 ATGCTTTGTCCTTGGGGTTC 58.367 50.000 0.00 0.00 0.00 3.62
4943 5836 0.893727 CTTTGTCCTTGGGGTTCGGG 60.894 60.000 0.00 0.00 0.00 5.14
4988 5888 6.199393 TCATCGTGTATGTTCTCTTCGTATG 58.801 40.000 0.00 0.00 36.89 2.39
5006 5906 4.093408 CGTATGACAGAAAACATGGGTCAG 59.907 45.833 0.00 0.00 41.27 3.51
5011 5911 4.023291 ACAGAAAACATGGGTCAGTTTGT 58.977 39.130 0.00 0.00 37.94 2.83
5012 5912 4.142182 ACAGAAAACATGGGTCAGTTTGTG 60.142 41.667 0.00 0.00 37.94 3.33
5013 5913 4.023291 AGAAAACATGGGTCAGTTTGTGT 58.977 39.130 0.00 0.00 37.94 3.72
5014 5914 3.799281 AAACATGGGTCAGTTTGTGTG 57.201 42.857 0.00 0.00 36.65 3.82
5015 5915 2.727123 ACATGGGTCAGTTTGTGTGA 57.273 45.000 0.00 0.00 0.00 3.58
5016 5916 3.228188 ACATGGGTCAGTTTGTGTGAT 57.772 42.857 0.00 0.00 0.00 3.06
5017 5917 3.565307 ACATGGGTCAGTTTGTGTGATT 58.435 40.909 0.00 0.00 0.00 2.57
5018 5918 3.318839 ACATGGGTCAGTTTGTGTGATTG 59.681 43.478 0.00 0.00 0.00 2.67
5236 6205 4.098044 CCAGAGGTCAGTTACGTACATGAT 59.902 45.833 11.04 0.00 0.00 2.45
5244 6213 5.410132 TCAGTTACGTACATGATTTTGGTGG 59.590 40.000 0.00 0.00 0.00 4.61
5275 6245 2.733858 GCTTCCACGCACAACTTTGAAA 60.734 45.455 0.00 0.00 0.00 2.69
5285 6255 7.378461 CACGCACAACTTTGAAAATAGTTACAT 59.622 33.333 0.00 0.00 33.49 2.29
5286 6256 7.378461 ACGCACAACTTTGAAAATAGTTACATG 59.622 33.333 0.00 0.00 33.49 3.21
5293 6263 4.020543 TGAAAATAGTTACATGGGGGTGC 58.979 43.478 0.00 0.00 0.00 5.01
5295 6265 4.331159 AAATAGTTACATGGGGGTGCTT 57.669 40.909 0.00 0.00 0.00 3.91
5298 6268 3.081710 AGTTACATGGGGGTGCTTTAC 57.918 47.619 0.00 0.00 0.00 2.01
5323 6293 4.799564 AGTGAAACACAAGGCAGAAAAA 57.200 36.364 4.75 0.00 41.43 1.94
5347 6317 7.793927 AATAGTAGCCTAAGCAACAAGAATC 57.206 36.000 0.00 0.00 43.56 2.52
5349 6319 5.560724 AGTAGCCTAAGCAACAAGAATCAA 58.439 37.500 0.00 0.00 43.56 2.57
5350 6320 5.645497 AGTAGCCTAAGCAACAAGAATCAAG 59.355 40.000 0.00 0.00 43.56 3.02
5351 6321 4.401925 AGCCTAAGCAACAAGAATCAAGT 58.598 39.130 0.00 0.00 43.56 3.16
5352 6322 4.217118 AGCCTAAGCAACAAGAATCAAGTG 59.783 41.667 0.00 0.00 43.56 3.16
5354 6324 4.082571 CCTAAGCAACAAGAATCAAGTGGG 60.083 45.833 0.00 0.00 0.00 4.61
5356 6326 3.565307 AGCAACAAGAATCAAGTGGGAA 58.435 40.909 0.00 0.00 0.00 3.97
5357 6327 3.571401 AGCAACAAGAATCAAGTGGGAAG 59.429 43.478 0.00 0.00 0.00 3.46
5358 6328 3.858503 GCAACAAGAATCAAGTGGGAAGC 60.859 47.826 0.00 0.00 0.00 3.86
5359 6329 2.519013 ACAAGAATCAAGTGGGAAGCC 58.481 47.619 0.00 0.00 0.00 4.35
5361 6331 2.751806 CAAGAATCAAGTGGGAAGCCTC 59.248 50.000 0.00 0.00 0.00 4.70
5381 6351 2.832129 TCTGAGCCCACGATAAAAGAGT 59.168 45.455 0.00 0.00 0.00 3.24
5384 6354 3.244422 TGAGCCCACGATAAAAGAGTTGT 60.244 43.478 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.328343 TGAATCGGTTGTTTCCCCTTAGA 59.672 43.478 0.00 0.00 0.00 2.10
8 9 2.626266 GTTGAATCGGTTGTTTCCCCTT 59.374 45.455 0.00 0.00 0.00 3.95
27 28 1.028905 CACACACGTTGGGAATGGTT 58.971 50.000 0.00 0.00 0.00 3.67
31 32 1.150536 AGCCACACACGTTGGGAAT 59.849 52.632 6.88 0.00 0.00 3.01
34 35 3.286751 CCAGCCACACACGTTGGG 61.287 66.667 6.88 0.40 0.00 4.12
41 42 0.616111 AAACAAACCCCAGCCACACA 60.616 50.000 0.00 0.00 0.00 3.72
44 45 2.224185 CCTTAAAACAAACCCCAGCCAC 60.224 50.000 0.00 0.00 0.00 5.01
48 49 5.163353 ACATGAACCTTAAAACAAACCCCAG 60.163 40.000 0.00 0.00 0.00 4.45
50 51 5.284861 ACATGAACCTTAAAACAAACCCC 57.715 39.130 0.00 0.00 0.00 4.95
60 61 6.094881 GCTTGCCTACATAACATGAACCTTAA 59.905 38.462 0.00 0.00 0.00 1.85
69 70 4.220693 TCACTGCTTGCCTACATAACAT 57.779 40.909 0.00 0.00 0.00 2.71
76 77 5.360591 AGTATGTATTCACTGCTTGCCTAC 58.639 41.667 0.00 0.00 0.00 3.18
77 78 5.614324 AGTATGTATTCACTGCTTGCCTA 57.386 39.130 0.00 0.00 0.00 3.93
93 95 7.971722 GCAAAAATGACCCGTTTAATAGTATGT 59.028 33.333 0.00 0.00 0.00 2.29
96 98 7.450124 TGCAAAAATGACCCGTTTAATAGTA 57.550 32.000 0.00 0.00 0.00 1.82
97 99 6.334102 TGCAAAAATGACCCGTTTAATAGT 57.666 33.333 0.00 0.00 0.00 2.12
100 102 5.546526 ACATGCAAAAATGACCCGTTTAAT 58.453 33.333 0.00 0.00 0.00 1.40
102 104 4.592485 ACATGCAAAAATGACCCGTTTA 57.408 36.364 0.00 0.00 0.00 2.01
110 112 3.139850 CAGCCCAAACATGCAAAAATGA 58.860 40.909 0.00 0.00 0.00 2.57
120 133 1.477553 CCTACATGCAGCCCAAACAT 58.522 50.000 0.00 0.00 0.00 2.71
123 136 1.076370 TGCCTACATGCAGCCCAAA 59.924 52.632 0.00 0.00 36.04 3.28
136 149 2.047274 GACGTGCTTGGCTGCCTA 60.047 61.111 21.03 11.84 0.00 3.93
142 155 2.596904 TATCTAAGGACGTGCTTGGC 57.403 50.000 29.82 0.00 0.00 4.52
147 160 8.463456 GTCCTATATTTTATCTAAGGACGTGC 57.537 38.462 0.00 0.00 42.45 5.34
303 324 1.211969 CAGGTCAGGTCGTACCACG 59.788 63.158 6.78 0.00 41.95 4.94
304 325 0.243095 GTCAGGTCAGGTCGTACCAC 59.757 60.000 6.78 0.00 41.95 4.16
305 326 0.896940 GGTCAGGTCAGGTCGTACCA 60.897 60.000 6.78 0.00 41.95 3.25
306 327 0.611340 AGGTCAGGTCAGGTCGTACC 60.611 60.000 0.00 0.00 38.99 3.34
308 329 2.224843 TGTTAGGTCAGGTCAGGTCGTA 60.225 50.000 0.00 0.00 0.00 3.43
309 330 1.254954 GTTAGGTCAGGTCAGGTCGT 58.745 55.000 0.00 0.00 0.00 4.34
310 331 1.254026 TGTTAGGTCAGGTCAGGTCG 58.746 55.000 0.00 0.00 0.00 4.79
311 332 3.369576 GGATTGTTAGGTCAGGTCAGGTC 60.370 52.174 0.00 0.00 0.00 3.85
312 333 2.572104 GGATTGTTAGGTCAGGTCAGGT 59.428 50.000 0.00 0.00 0.00 4.00
313 334 2.840651 AGGATTGTTAGGTCAGGTCAGG 59.159 50.000 0.00 0.00 0.00 3.86
314 335 3.866651 CAGGATTGTTAGGTCAGGTCAG 58.133 50.000 0.00 0.00 0.00 3.51
315 336 2.027192 GCAGGATTGTTAGGTCAGGTCA 60.027 50.000 0.00 0.00 0.00 4.02
339 360 4.249513 GGAAGGAGAATGCCTGCC 57.750 61.111 0.00 0.00 46.55 4.85
340 361 1.454663 GGGGAAGGAGAATGCCTGC 60.455 63.158 0.00 0.00 38.58 4.85
341 362 1.228510 GGGGGAAGGAGAATGCCTG 59.771 63.158 0.00 0.00 38.58 4.85
342 363 0.850883 TTGGGGGAAGGAGAATGCCT 60.851 55.000 0.00 0.00 40.93 4.75
445 481 1.603172 GGATGGGATGATGACGACGAC 60.603 57.143 0.00 0.00 0.00 4.34
594 634 0.036294 GAGAACGGAAGAACTGGGGG 60.036 60.000 0.00 0.00 0.00 5.40
599 639 4.757149 CCAAGAAATGAGAACGGAAGAACT 59.243 41.667 0.00 0.00 0.00 3.01
615 655 0.539438 ATGCAACCTCGCCCAAGAAA 60.539 50.000 0.00 0.00 0.00 2.52
744 784 2.022195 CCCTGTCGACGAGATTAGGAA 58.978 52.381 16.67 0.00 37.92 3.36
917 957 0.114560 AGAAACGAGGAGGGGTCAGA 59.885 55.000 0.00 0.00 0.00 3.27
1440 1487 2.818274 CTGATGAGCTGCGCTGCA 60.818 61.111 35.70 20.24 39.88 4.41
1512 1559 0.608640 GGAAGTTCTCCGGCTTGAGA 59.391 55.000 0.00 0.00 39.58 3.27
1560 1607 1.200020 CCAAAATCGGTGGTCTTGAGC 59.800 52.381 0.00 0.00 0.00 4.26
1635 1682 9.257651 ACTACACATGAAAGAACAAAGTACTAC 57.742 33.333 0.00 0.00 0.00 2.73
1655 1707 5.051240 CGAACTGGTCAACAAAGTACTACAC 60.051 44.000 0.00 0.00 0.00 2.90
1915 2021 3.287222 ACCACACAATAACACAAGCACT 58.713 40.909 0.00 0.00 0.00 4.40
2005 2111 4.263435 ACAAAGTTACACGGTTCCTTTCA 58.737 39.130 0.00 0.00 0.00 2.69
2067 2239 2.550830 ATGAACGCACTTGTCTTCCT 57.449 45.000 0.00 0.00 0.00 3.36
2080 2252 5.063438 CCAGTGTTGTCTGGTTATATGAACG 59.937 44.000 4.75 0.00 46.92 3.95
2316 2680 2.565391 TCAACAAATCTAGTCCGGCTCA 59.435 45.455 0.00 0.00 0.00 4.26
2322 2686 8.443953 AGCAGATATTTCAACAAATCTAGTCC 57.556 34.615 0.00 0.00 33.95 3.85
2757 3574 5.487488 ACCAAATCTACCAGTTCCATGAGTA 59.513 40.000 0.00 0.00 0.00 2.59
2768 3585 5.245531 TGTCTAAAGCACCAAATCTACCAG 58.754 41.667 0.00 0.00 0.00 4.00
2993 3847 5.895636 TTCTGCTCAAAAAGAAGTTGTGA 57.104 34.783 0.00 0.00 31.68 3.58
3514 4398 3.372025 GCCATAAACCCTCAAGACTCCAT 60.372 47.826 0.00 0.00 0.00 3.41
3799 4687 6.127253 CCATTAAAGCCTGGATTTCATGTTCT 60.127 38.462 22.79 0.00 34.24 3.01
3860 4748 5.674933 ACTCGTTTTCTGAATGAAGGAAC 57.325 39.130 0.00 0.00 35.89 3.62
3934 4823 0.604073 TGTTGTCGATGTCCGCCTTA 59.396 50.000 0.00 0.00 38.37 2.69
4199 5088 6.489700 TCGAACAAAACATATATGCATGGGAT 59.510 34.615 10.16 0.00 0.00 3.85
4299 5188 1.599240 GCCCTTCCTCATCATCGCC 60.599 63.158 0.00 0.00 0.00 5.54
4311 5200 4.133796 GCACCCGCATTGCCCTTC 62.134 66.667 2.41 0.00 38.36 3.46
4450 5339 3.916761 TGATCAGGCATGCAAAAACTTC 58.083 40.909 21.36 7.08 0.00 3.01
4483 5372 6.106407 TCTCCCTTTCCCTCTTAGATTAGT 57.894 41.667 0.00 0.00 0.00 2.24
4484 5373 8.174085 TCTATCTCCCTTTCCCTCTTAGATTAG 58.826 40.741 0.00 0.00 0.00 1.73
4485 5374 8.070062 TCTATCTCCCTTTCCCTCTTAGATTA 57.930 38.462 0.00 0.00 0.00 1.75
4622 5512 4.761739 CAGTGTTCAACCACAGGAATACAT 59.238 41.667 0.00 0.00 37.53 2.29
4671 5561 8.556213 ACAGTAAACAGAAGTGACAGTAAAAA 57.444 30.769 0.00 0.00 0.00 1.94
4819 5709 8.031864 TGTTTGAAAATAGTTTCTTTGTGCAGA 58.968 29.630 15.90 0.00 43.13 4.26
4866 5757 9.445786 CGGACATGTTTATGGTAAATTGATAAC 57.554 33.333 0.00 0.00 38.66 1.89
4921 5813 1.632589 GAACCCCAAGGACAAAGCAT 58.367 50.000 0.00 0.00 36.73 3.79
4922 5814 0.821711 CGAACCCCAAGGACAAAGCA 60.822 55.000 0.00 0.00 36.73 3.91
4923 5815 1.524008 CCGAACCCCAAGGACAAAGC 61.524 60.000 0.00 0.00 36.73 3.51
4924 5816 0.893727 CCCGAACCCCAAGGACAAAG 60.894 60.000 0.00 0.00 36.73 2.77
4927 5819 3.961414 GCCCGAACCCCAAGGACA 61.961 66.667 0.00 0.00 36.73 4.02
4936 5829 1.893137 AGAAAATCAAAGGCCCGAACC 59.107 47.619 0.00 0.00 0.00 3.62
4940 5833 3.658757 TTTCAGAAAATCAAAGGCCCG 57.341 42.857 0.00 0.00 0.00 6.13
4963 5856 5.250235 ACGAAGAGAACATACACGATGAT 57.750 39.130 0.00 0.00 39.06 2.45
4988 5888 4.097892 ACAAACTGACCCATGTTTTCTGTC 59.902 41.667 0.00 0.00 34.60 3.51
5116 6018 7.744087 ACAGAATTTCAGTACACATTGCTAA 57.256 32.000 0.00 0.00 0.00 3.09
5170 6128 9.754382 TCGTTTTGAATGTATATAAGGTAGACC 57.246 33.333 0.00 0.00 0.00 3.85
5182 6151 3.308866 GCTACGGCTCGTTTTGAATGTAT 59.691 43.478 5.57 0.00 41.54 2.29
5183 6152 2.669434 GCTACGGCTCGTTTTGAATGTA 59.331 45.455 5.57 0.00 41.54 2.29
5184 6153 1.463444 GCTACGGCTCGTTTTGAATGT 59.537 47.619 5.57 0.00 41.54 2.71
5227 6196 5.049060 TCTGTTTCCACCAAAATCATGTACG 60.049 40.000 0.00 0.00 0.00 3.67
5228 6197 6.206634 TCTCTGTTTCCACCAAAATCATGTAC 59.793 38.462 0.00 0.00 0.00 2.90
5229 6198 6.303054 TCTCTGTTTCCACCAAAATCATGTA 58.697 36.000 0.00 0.00 0.00 2.29
5230 6199 5.139727 TCTCTGTTTCCACCAAAATCATGT 58.860 37.500 0.00 0.00 0.00 3.21
5236 6205 3.297134 AGCTCTCTGTTTCCACCAAAA 57.703 42.857 0.00 0.00 0.00 2.44
5244 6213 0.793250 GCGTGGAAGCTCTCTGTTTC 59.207 55.000 0.00 0.00 35.52 2.78
5275 6245 4.331159 AAAGCACCCCCATGTAACTATT 57.669 40.909 0.00 0.00 0.00 1.73
5285 6255 1.145571 ACTTCTGTAAAGCACCCCCA 58.854 50.000 0.00 0.00 0.00 4.96
5286 6256 1.073284 TCACTTCTGTAAAGCACCCCC 59.927 52.381 0.00 0.00 0.00 5.40
5293 6263 5.163663 TGCCTTGTGTTTCACTTCTGTAAAG 60.164 40.000 1.72 0.00 35.11 1.85
5295 6265 4.265893 TGCCTTGTGTTTCACTTCTGTAA 58.734 39.130 1.72 0.00 35.11 2.41
5298 6268 2.945008 TCTGCCTTGTGTTTCACTTCTG 59.055 45.455 1.72 0.00 35.11 3.02
5323 6293 7.338710 TGATTCTTGTTGCTTAGGCTACTATT 58.661 34.615 12.19 0.00 42.84 1.73
5324 6294 6.889198 TGATTCTTGTTGCTTAGGCTACTAT 58.111 36.000 12.19 2.01 42.84 2.12
5332 6302 4.761739 TCCCACTTGATTCTTGTTGCTTAG 59.238 41.667 0.00 0.00 0.00 2.18
5340 6310 2.751806 GAGGCTTCCCACTTGATTCTTG 59.248 50.000 0.00 0.00 0.00 3.02
5347 6317 0.676151 GCTCAGAGGCTTCCCACTTG 60.676 60.000 0.00 0.00 28.70 3.16
5349 6319 2.297129 GGCTCAGAGGCTTCCCACT 61.297 63.158 16.80 0.00 37.85 4.00
5350 6320 2.270527 GGCTCAGAGGCTTCCCAC 59.729 66.667 16.80 0.00 37.85 4.61
5351 6321 3.011517 GGGCTCAGAGGCTTCCCA 61.012 66.667 22.57 0.00 41.09 4.37
5352 6322 3.011517 TGGGCTCAGAGGCTTCCC 61.012 66.667 22.57 13.15 41.09 3.97
5354 6324 1.965754 ATCGTGGGCTCAGAGGCTTC 61.966 60.000 22.57 14.47 41.09 3.86
5356 6326 0.687757 TTATCGTGGGCTCAGAGGCT 60.688 55.000 22.57 5.96 41.09 4.58
5357 6327 0.178068 TTTATCGTGGGCTCAGAGGC 59.822 55.000 15.82 15.82 40.51 4.70
5358 6328 2.168521 TCTTTTATCGTGGGCTCAGAGG 59.831 50.000 0.00 0.00 0.00 3.69
5359 6329 3.118956 ACTCTTTTATCGTGGGCTCAGAG 60.119 47.826 0.00 0.00 34.02 3.35
5361 6331 3.252974 ACTCTTTTATCGTGGGCTCAG 57.747 47.619 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.