Multiple sequence alignment - TraesCS6D01G226800

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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 TraesCS6D01G226800 chr6D 100.000 5180 0 0 1 5180 318344549 318349728 0.000000e+00 9566.0
1 TraesCS6D01G226800 chr6B 96.660 3174 82 11 2022 5180 505802728 505799564 0.000000e+00 5252.0
2 TraesCS6D01G226800 chr6B 96.237 1196 28 8 845 2037 505803926 505802745 0.000000e+00 1943.0
3 TraesCS6D01G226800 chr6B 87.240 337 29 6 527 853 505805168 505804836 6.330000e-99 372.0
4 TraesCS6D01G226800 chr6A 94.687 3068 131 17 2132 5180 455937938 455940992 0.000000e+00 4734.0
5 TraesCS6D01G226800 chr6A 95.212 1295 48 7 836 2127 455936543 455937826 0.000000e+00 2036.0
6 TraesCS6D01G226800 chr6A 88.102 706 65 8 137 826 455927474 455928176 0.000000e+00 821.0
7 TraesCS6D01G226800 chr6A 88.372 86 8 2 1253 1337 503829287 503829371 9.180000e-18 102.0
8 TraesCS6D01G226800 chr6A 90.000 80 6 2 1259 1337 602319905 602319827 9.180000e-18 102.0
9 TraesCS6D01G226800 chr7A 84.199 443 66 4 4714 5154 437610771 437610331 1.330000e-115 427.0
10 TraesCS6D01G226800 chr7A 89.552 67 7 0 2078 2144 74549638 74549704 9.240000e-13 86.1
11 TraesCS6D01G226800 chr7D 83.296 443 70 4 4714 5154 387496143 387495703 6.250000e-109 405.0
12 TraesCS6D01G226800 chr7D 94.828 58 3 0 2087 2144 212881156 212881213 1.990000e-14 91.6
13 TraesCS6D01G226800 chr7B 84.086 421 63 4 4714 5132 382521062 382520644 2.250000e-108 403.0
14 TraesCS6D01G226800 chr1D 90.260 154 15 0 2248 2401 482899996 482899843 8.800000e-48 202.0
15 TraesCS6D01G226800 chr1D 93.443 61 4 0 2084 2144 59876036 59875976 1.990000e-14 91.6
16 TraesCS6D01G226800 chr2A 85.475 179 19 4 2248 2420 298635236 298635059 4.120000e-41 180.0
17 TraesCS6D01G226800 chr4A 79.679 187 29 6 2504 2683 713895273 713895089 5.450000e-25 126.0
18 TraesCS6D01G226800 chr5D 77.209 215 35 8 2515 2719 498660546 498660756 4.240000e-21 113.0
19 TraesCS6D01G226800 chr3D 93.939 66 4 0 2079 2144 324311174 324311109 3.300000e-17 100.0
20 TraesCS6D01G226800 chr3A 92.424 66 5 0 2079 2144 397141363 397141428 1.540000e-15 95.3
21 TraesCS6D01G226800 chr5A 93.548 62 3 1 2086 2146 48921388 48921449 1.990000e-14 91.6
22 TraesCS6D01G226800 chr3B 90.909 66 6 0 2079 2144 394954539 394954604 7.140000e-14 89.8
23 TraesCS6D01G226800 chr1B 92.453 53 4 0 4481 4533 390622352 390622300 5.560000e-10 76.8
24 TraesCS6D01G226800 chr2B 87.719 57 7 0 4481 4537 53472944 53473000 3.350000e-07 67.6
25 TraesCS6D01G226800 chr4D 94.595 37 2 0 4485 4521 43670375 43670339 2.010000e-04 58.4


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 TraesCS6D01G226800 chr6D 318344549 318349728 5179 False 9566.000000 9566 100.0000 1 5180 1 chr6D.!!$F1 5179
1 TraesCS6D01G226800 chr6B 505799564 505805168 5604 True 2522.333333 5252 93.3790 527 5180 3 chr6B.!!$R1 4653
2 TraesCS6D01G226800 chr6A 455936543 455940992 4449 False 3385.000000 4734 94.9495 836 5180 2 chr6A.!!$F3 4344
3 TraesCS6D01G226800 chr6A 455927474 455928176 702 False 821.000000 821 88.1020 137 826 1 chr6A.!!$F1 689

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
87 88 0.107017 CAATGCCAGGGAGGTGTAGG 60.107 60.0 0.00 0.0 40.61 3.18 F
1343 2289 0.106868 CATCTGGCCTGGAGCAATCA 60.107 55.0 10.07 0.0 46.50 2.57 F
1346 2292 0.822532 CTGGCCTGGAGCAATCATCC 60.823 60.0 3.32 0.0 46.50 3.51 F
3305 4406 0.109781 CACGCAATTTTCCCACTCCG 60.110 55.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 2302 0.891373 TCCAGTGCAGACTACAGAGC 59.109 55.000 0.00 0.00 0.00 4.09 R
2900 3990 1.308998 CTGGACTGGGTTGTGACAAC 58.691 55.000 19.59 19.59 0.00 3.32 R
3321 4422 5.345702 CATGAAGTGTGCCCATGATTTTAG 58.654 41.667 0.00 0.00 39.86 1.85 R
5040 6152 1.446792 CGTCTACACCTGGCTGCTG 60.447 63.158 0.00 0.00 0.00 4.41 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
20 21 2.550830 GTGGATCTCACACACCACTT 57.449 50.000 0.00 0.00 46.14 3.16
21 22 2.417719 GTGGATCTCACACACCACTTC 58.582 52.381 0.00 0.00 46.14 3.01
22 23 1.347707 TGGATCTCACACACCACTTCC 59.652 52.381 0.00 0.00 0.00 3.46
23 24 1.347707 GGATCTCACACACCACTTCCA 59.652 52.381 0.00 0.00 0.00 3.53
24 25 2.026822 GGATCTCACACACCACTTCCAT 60.027 50.000 0.00 0.00 0.00 3.41
25 26 2.549064 TCTCACACACCACTTCCATG 57.451 50.000 0.00 0.00 0.00 3.66
26 27 1.072173 TCTCACACACCACTTCCATGG 59.928 52.381 4.97 4.97 46.10 3.66
33 34 2.946947 CCACTTCCATGGTGTGACC 58.053 57.895 28.92 0.00 39.22 4.02
53 54 4.755266 CCACAACTATGGTTAGCTAGGT 57.245 45.455 0.00 0.00 34.77 3.08
54 55 4.694339 CCACAACTATGGTTAGCTAGGTC 58.306 47.826 0.00 0.00 34.77 3.85
55 56 4.360563 CACAACTATGGTTAGCTAGGTCG 58.639 47.826 0.00 0.00 33.88 4.79
56 57 4.097437 CACAACTATGGTTAGCTAGGTCGA 59.903 45.833 0.00 0.00 33.88 4.20
57 58 4.894114 ACAACTATGGTTAGCTAGGTCGAT 59.106 41.667 0.00 0.00 33.88 3.59
58 59 5.221263 ACAACTATGGTTAGCTAGGTCGATG 60.221 44.000 0.00 0.00 33.88 3.84
59 60 2.821991 ATGGTTAGCTAGGTCGATGC 57.178 50.000 0.00 0.00 0.00 3.91
60 61 0.384309 TGGTTAGCTAGGTCGATGCG 59.616 55.000 0.00 0.00 0.00 4.73
61 62 0.318784 GGTTAGCTAGGTCGATGCGG 60.319 60.000 0.00 0.00 0.00 5.69
62 63 0.384669 GTTAGCTAGGTCGATGCGGT 59.615 55.000 0.00 0.00 0.00 5.68
63 64 1.605710 GTTAGCTAGGTCGATGCGGTA 59.394 52.381 0.00 0.00 0.00 4.02
64 65 1.520494 TAGCTAGGTCGATGCGGTAG 58.480 55.000 0.00 0.00 0.00 3.18
65 66 1.371881 GCTAGGTCGATGCGGTAGC 60.372 63.158 0.00 0.00 45.41 3.58
84 85 2.036256 GCAATGCCAGGGAGGTGT 59.964 61.111 0.00 0.00 40.61 4.16
85 86 1.302949 GCAATGCCAGGGAGGTGTA 59.697 57.895 0.00 0.00 40.61 2.90
86 87 0.749454 GCAATGCCAGGGAGGTGTAG 60.749 60.000 0.00 0.00 40.61 2.74
87 88 0.107017 CAATGCCAGGGAGGTGTAGG 60.107 60.000 0.00 0.00 40.61 3.18
88 89 0.253160 AATGCCAGGGAGGTGTAGGA 60.253 55.000 0.00 0.00 40.61 2.94
89 90 0.983378 ATGCCAGGGAGGTGTAGGAC 60.983 60.000 0.00 0.00 40.61 3.85
90 91 2.722201 GCCAGGGAGGTGTAGGACG 61.722 68.421 0.00 0.00 40.61 4.79
91 92 2.722201 CCAGGGAGGTGTAGGACGC 61.722 68.421 0.00 0.00 0.00 5.19
92 93 1.982395 CAGGGAGGTGTAGGACGCA 60.982 63.158 0.00 0.00 0.00 5.24
93 94 1.682684 AGGGAGGTGTAGGACGCAG 60.683 63.158 0.00 0.00 0.00 5.18
94 95 2.184579 GGAGGTGTAGGACGCAGC 59.815 66.667 0.00 0.00 34.87 5.25
95 96 2.184579 GAGGTGTAGGACGCAGCC 59.815 66.667 0.00 0.00 35.19 4.85
96 97 2.603473 AGGTGTAGGACGCAGCCA 60.603 61.111 0.00 0.00 35.19 4.75
97 98 1.961180 GAGGTGTAGGACGCAGCCAT 61.961 60.000 0.00 0.00 35.19 4.40
98 99 1.521681 GGTGTAGGACGCAGCCATC 60.522 63.158 0.00 0.00 0.00 3.51
99 100 1.521681 GTGTAGGACGCAGCCATCC 60.522 63.158 2.48 2.48 34.98 3.51
100 101 2.279517 GTAGGACGCAGCCATCCG 60.280 66.667 4.95 0.00 40.20 4.18
101 102 4.221422 TAGGACGCAGCCATCCGC 62.221 66.667 4.95 0.00 40.20 5.54
105 106 4.783621 ACGCAGCCATCCGCACAT 62.784 61.111 0.00 0.00 41.38 3.21
106 107 4.246206 CGCAGCCATCCGCACATG 62.246 66.667 0.00 0.00 41.38 3.21
107 108 2.825387 GCAGCCATCCGCACATGA 60.825 61.111 0.00 0.00 41.38 3.07
108 109 2.831366 GCAGCCATCCGCACATGAG 61.831 63.158 0.00 0.00 41.38 2.90
109 110 2.184830 CAGCCATCCGCACATGAGG 61.185 63.158 0.00 0.00 41.38 3.86
110 111 2.903855 GCCATCCGCACATGAGGG 60.904 66.667 0.00 0.00 36.76 4.30
111 112 2.591753 CCATCCGCACATGAGGGT 59.408 61.111 0.00 0.00 35.57 4.34
112 113 1.829456 CCATCCGCACATGAGGGTA 59.171 57.895 0.00 0.00 35.57 3.69
113 114 0.397941 CCATCCGCACATGAGGGTAT 59.602 55.000 0.00 0.00 35.57 2.73
114 115 1.516161 CATCCGCACATGAGGGTATG 58.484 55.000 0.00 0.00 35.57 2.39
115 116 0.250467 ATCCGCACATGAGGGTATGC 60.250 55.000 0.00 0.00 35.57 3.14
117 118 3.736483 GCACATGAGGGTATGCGG 58.264 61.111 0.00 0.00 0.00 5.69
118 119 2.546494 GCACATGAGGGTATGCGGC 61.546 63.158 0.00 0.00 0.00 6.53
119 120 2.108976 ACATGAGGGTATGCGGCG 59.891 61.111 0.51 0.51 0.00 6.46
120 121 2.666190 CATGAGGGTATGCGGCGG 60.666 66.667 9.78 0.00 0.00 6.13
121 122 3.941188 ATGAGGGTATGCGGCGGG 61.941 66.667 9.78 0.00 0.00 6.13
163 164 1.852989 GCTCGCAGCGTTATACGACG 61.853 60.000 15.93 0.00 46.05 5.12
173 174 0.373370 TTATACGACGACGGACACGG 59.627 55.000 12.58 0.00 46.48 4.94
174 175 0.739462 TATACGACGACGGACACGGT 60.739 55.000 12.58 0.00 46.48 4.83
196 197 1.594293 CCGGGCATCGACATGGTAC 60.594 63.158 0.00 0.00 42.43 3.34
251 252 2.660064 GGTGGCTCTGGACGATGGT 61.660 63.158 0.00 0.00 0.00 3.55
297 298 3.978272 GCCCAGAGCTTGTGTCAG 58.022 61.111 0.00 0.00 38.99 3.51
300 301 1.301244 CCAGAGCTTGTGTCAGCGT 60.301 57.895 0.00 0.00 45.24 5.07
306 307 1.374758 CTTGTGTCAGCGTCCTCCC 60.375 63.158 0.00 0.00 0.00 4.30
308 309 3.311110 GTGTCAGCGTCCTCCCCA 61.311 66.667 0.00 0.00 0.00 4.96
316 317 2.427245 CGTCCTCCCCACCTAGCAG 61.427 68.421 0.00 0.00 0.00 4.24
320 321 1.687146 CTCCCCACCTAGCAGCTCA 60.687 63.158 0.00 0.00 0.00 4.26
323 324 1.220206 CCCACCTAGCAGCTCACAG 59.780 63.158 0.00 0.00 0.00 3.66
326 327 1.186200 CACCTAGCAGCTCACAGGTA 58.814 55.000 14.07 0.00 39.40 3.08
365 366 2.358737 GTGTCCTTGAGGCACCGG 60.359 66.667 0.00 0.00 36.73 5.28
389 390 1.098050 GTCATGACATGCCCTTCCAC 58.902 55.000 21.07 0.00 0.00 4.02
391 392 0.677731 CATGACATGCCCTTCCACGT 60.678 55.000 1.71 0.00 0.00 4.49
395 396 2.045926 ATGCCCTTCCACGTCAGC 60.046 61.111 0.00 0.00 0.00 4.26
406 407 2.202440 CGTCAGCGTCGTGTAGGG 60.202 66.667 0.00 0.00 0.00 3.53
433 434 0.394352 GCCCTGAAATCCATCACCGT 60.394 55.000 0.00 0.00 0.00 4.83
444 445 0.173481 CATCACCGTCTCGACATGGT 59.827 55.000 0.00 0.00 34.29 3.55
445 446 0.456221 ATCACCGTCTCGACATGGTC 59.544 55.000 0.99 0.00 30.72 4.02
461 462 3.077556 TCTTCAGGAGGGAGGCGC 61.078 66.667 0.00 0.00 0.00 6.53
462 463 4.521062 CTTCAGGAGGGAGGCGCG 62.521 72.222 0.00 0.00 0.00 6.86
540 541 2.672996 GCGAGGGGCAAAGCTCAA 60.673 61.111 0.00 0.00 42.87 3.02
557 558 1.988406 AAGCGGAGGTAGGGTGGTC 60.988 63.158 0.00 0.00 37.06 4.02
619 625 2.414785 GCGCCGGTGAATTGGGAAT 61.415 57.895 21.76 0.00 0.00 3.01
633 639 8.773645 GTGAATTGGGAATTTTCTTTTACCAAG 58.226 33.333 6.30 0.00 39.56 3.61
689 702 6.017687 GTCAGTACGGTTAAAGACAAAACCAT 60.018 38.462 5.21 0.00 44.49 3.55
714 727 6.659242 TCTCAAATTATGTCCAAAACCTCTCC 59.341 38.462 0.00 0.00 0.00 3.71
721 734 1.202842 TCCAAAACCTCTCCGGGAAAC 60.203 52.381 0.00 0.00 36.97 2.78
812 836 5.357032 AGGATTACAATCGGATGAAACCAAC 59.643 40.000 0.00 0.00 36.27 3.77
913 1858 5.074652 TCTCTACTGTATATGGTACTGGGCT 59.925 44.000 0.00 0.00 0.00 5.19
1193 2139 2.435693 CGATTCTCCCTTCCGCCCT 61.436 63.158 0.00 0.00 0.00 5.19
1204 2150 2.444706 CCGCCCTCCTCAGATCCA 60.445 66.667 0.00 0.00 0.00 3.41
1222 2168 6.261826 CAGATCCATGAATTACTTGGGACTTC 59.738 42.308 0.00 0.00 42.06 3.01
1251 2197 2.222596 CGTTGCTGCTCGATACTTTGTC 60.223 50.000 11.00 0.00 0.00 3.18
1284 2230 1.808945 CGACTGATTTTGAGCTTGCCT 59.191 47.619 0.00 0.00 0.00 4.75
1343 2289 0.106868 CATCTGGCCTGGAGCAATCA 60.107 55.000 10.07 0.00 46.50 2.57
1346 2292 0.822532 CTGGCCTGGAGCAATCATCC 60.823 60.000 3.32 0.00 46.50 3.51
1354 2300 2.362397 TGGAGCAATCATCCGTACTCTC 59.638 50.000 0.00 0.00 39.91 3.20
1356 2302 3.551863 GGAGCAATCATCCGTACTCTCTG 60.552 52.174 0.00 0.00 0.00 3.35
1357 2303 2.131183 GCAATCATCCGTACTCTCTGC 58.869 52.381 0.00 0.00 0.00 4.26
1362 2308 2.020720 CATCCGTACTCTCTGCTCTGT 58.979 52.381 0.00 0.00 0.00 3.41
1364 2310 2.907634 TCCGTACTCTCTGCTCTGTAG 58.092 52.381 0.00 0.00 0.00 2.74
1366 2312 2.610374 CCGTACTCTCTGCTCTGTAGTC 59.390 54.545 0.00 0.00 0.00 2.59
1367 2313 3.527533 CGTACTCTCTGCTCTGTAGTCT 58.472 50.000 0.00 0.00 0.00 3.24
1368 2314 3.308595 CGTACTCTCTGCTCTGTAGTCTG 59.691 52.174 0.00 0.00 0.00 3.51
1369 2315 2.091541 ACTCTCTGCTCTGTAGTCTGC 58.908 52.381 0.00 0.00 0.00 4.26
1370 2316 2.090760 CTCTCTGCTCTGTAGTCTGCA 58.909 52.381 0.00 0.00 0.00 4.41
1390 2336 2.818432 CACTGGAGTAGTAGTCCGTGTT 59.182 50.000 25.30 9.39 40.67 3.32
1578 2524 3.695060 CGAGACTTTGTAGCCTCCTTCTA 59.305 47.826 0.00 0.00 27.79 2.10
1610 2556 5.766150 TTTGTTGAACCACATGTAAGAGG 57.234 39.130 0.00 0.00 0.00 3.69
1621 2567 4.690748 CACATGTAAGAGGTACAAGGTGTG 59.309 45.833 0.00 8.12 45.81 3.82
1636 2582 6.173339 ACAAGGTGTGTTTCTGGATGTATAG 58.827 40.000 0.00 0.00 37.01 1.31
1640 2586 6.099701 AGGTGTGTTTCTGGATGTATAGCATA 59.900 38.462 0.00 0.00 38.06 3.14
1694 2640 8.806146 ACTATCTGACAAATTTAGCCATTTTGT 58.194 29.630 6.32 6.32 44.02 2.83
2037 2983 6.077993 AGGATTACATAGTCTATGGCTGTCA 58.922 40.000 21.32 0.00 40.47 3.58
2228 3313 7.201884 GGTGCTTCTTTTATTTCCTATAACCCC 60.202 40.741 0.00 0.00 0.00 4.95
3305 4406 0.109781 CACGCAATTTTCCCACTCCG 60.110 55.000 0.00 0.00 0.00 4.63
3321 4422 3.603770 CACTCCGCAACATTTCGATTTTC 59.396 43.478 0.00 0.00 0.00 2.29
3466 4567 8.158132 TGTTATCCAAATTGTACCACTCTGTTA 58.842 33.333 0.00 0.00 0.00 2.41
3762 4863 6.014327 AGAGGTAAAATAGACCACGTACCAAA 60.014 38.462 0.00 0.00 39.65 3.28
3868 4969 4.153411 AGAAGTCTCGAAAGAAGAGGGAA 58.847 43.478 0.00 0.00 41.32 3.97
4129 5230 8.340757 TGGTATTTGTATATTTCCTGACCCTTT 58.659 33.333 0.00 0.00 0.00 3.11
4171 5272 1.064463 AGGCATGGTAACCCAGACATG 60.064 52.381 0.00 0.00 46.15 3.21
4194 5295 5.985530 TGTTAGTGACACATTTGAGACTGAG 59.014 40.000 8.59 0.00 32.00 3.35
4261 5366 5.521010 TCGATGTTGTCTTTGTTACGAACTT 59.479 36.000 0.00 0.00 0.00 2.66
4279 5384 5.334802 CGAACTTCATATGTTGCCTTTGTGA 60.335 40.000 1.90 0.00 0.00 3.58
4286 5391 7.053498 TCATATGTTGCCTTTGTGATAGCTAA 58.947 34.615 0.00 0.00 0.00 3.09
4306 5411 7.323420 AGCTAAAAATTTCATTAGGAAGTGCC 58.677 34.615 10.30 0.00 36.72 5.01
4403 5508 5.939764 ACATTGCAGGACAGATAAGAGTA 57.060 39.130 0.00 0.00 0.00 2.59
4410 5515 9.905713 TTGCAGGACAGATAAGAGTAATAATTT 57.094 29.630 0.00 0.00 0.00 1.82
4533 5645 7.106239 AGAACATCTTCTATTTGTGAACGGAT 58.894 34.615 0.00 0.00 34.74 4.18
4589 5701 3.743911 CGGTTTAATTTTGGGCAAGAACC 59.256 43.478 0.00 0.00 33.67 3.62
4590 5702 4.709250 GGTTTAATTTTGGGCAAGAACCA 58.291 39.130 0.00 0.00 36.27 3.67
4628 5740 1.334869 CCTTCTTTTGTTCAGCGTGCT 59.665 47.619 0.00 0.00 0.00 4.40
4691 5803 0.396974 AGGTTTTCTGCAAGCCCACA 60.397 50.000 0.00 0.00 36.38 4.17
4693 5805 1.892474 GGTTTTCTGCAAGCCCACATA 59.108 47.619 0.00 0.00 29.24 2.29
4808 5920 0.249531 TTGTTGTAGGCTGCGACGAA 60.250 50.000 16.74 10.10 0.00 3.85
4809 5921 0.666274 TGTTGTAGGCTGCGACGAAG 60.666 55.000 16.74 0.00 0.00 3.79
4845 5957 1.008538 CAGAACGCCAACCTTGTGC 60.009 57.895 0.00 0.00 0.00 4.57
5040 6152 3.917760 ATGAGCGCCGAGTAGCCC 61.918 66.667 2.29 0.00 0.00 5.19
5151 6263 2.087009 CGAGAACGTGAACCTCCGC 61.087 63.158 0.00 0.00 34.56 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.347707 GGAAGTGGTGTGTGAGATCCA 59.652 52.381 0.00 0.00 0.00 3.41
3 4 1.347707 TGGAAGTGGTGTGTGAGATCC 59.652 52.381 0.00 0.00 0.00 3.36
4 5 2.839486 TGGAAGTGGTGTGTGAGATC 57.161 50.000 0.00 0.00 0.00 2.75
5 6 2.290514 CCATGGAAGTGGTGTGTGAGAT 60.291 50.000 5.56 0.00 34.46 2.75
6 7 1.072173 CCATGGAAGTGGTGTGTGAGA 59.928 52.381 5.56 0.00 34.46 3.27
7 8 1.527034 CCATGGAAGTGGTGTGTGAG 58.473 55.000 5.56 0.00 34.46 3.51
8 9 3.723772 CCATGGAAGTGGTGTGTGA 57.276 52.632 5.56 0.00 34.46 3.58
15 16 0.110295 TGGTCACACCATGGAAGTGG 59.890 55.000 28.86 17.24 44.79 4.00
16 17 3.723772 TGGTCACACCATGGAAGTG 57.276 52.632 25.95 25.95 44.79 3.16
32 33 4.694339 GACCTAGCTAACCATAGTTGTGG 58.306 47.826 0.00 0.00 45.04 4.17
33 34 4.097437 TCGACCTAGCTAACCATAGTTGTG 59.903 45.833 0.00 0.00 36.68 3.33
34 35 4.275810 TCGACCTAGCTAACCATAGTTGT 58.724 43.478 0.00 0.00 36.68 3.32
35 36 4.913335 TCGACCTAGCTAACCATAGTTG 57.087 45.455 0.00 0.00 36.68 3.16
36 37 4.262079 GCATCGACCTAGCTAACCATAGTT 60.262 45.833 0.00 0.00 40.15 2.24
37 38 3.256136 GCATCGACCTAGCTAACCATAGT 59.744 47.826 0.00 0.00 0.00 2.12
38 39 3.670895 CGCATCGACCTAGCTAACCATAG 60.671 52.174 0.00 0.00 0.00 2.23
39 40 2.228103 CGCATCGACCTAGCTAACCATA 59.772 50.000 0.00 0.00 0.00 2.74
40 41 1.000163 CGCATCGACCTAGCTAACCAT 60.000 52.381 0.00 0.00 0.00 3.55
41 42 0.384309 CGCATCGACCTAGCTAACCA 59.616 55.000 0.00 0.00 0.00 3.67
42 43 0.318784 CCGCATCGACCTAGCTAACC 60.319 60.000 0.00 0.00 0.00 2.85
43 44 0.384669 ACCGCATCGACCTAGCTAAC 59.615 55.000 0.00 0.00 0.00 2.34
44 45 1.878088 CTACCGCATCGACCTAGCTAA 59.122 52.381 0.00 0.00 0.00 3.09
45 46 1.520494 CTACCGCATCGACCTAGCTA 58.480 55.000 0.00 0.00 0.00 3.32
46 47 1.797211 GCTACCGCATCGACCTAGCT 61.797 60.000 0.00 0.00 35.78 3.32
47 48 1.371881 GCTACCGCATCGACCTAGC 60.372 63.158 0.00 0.00 35.78 3.42
48 49 1.082038 CGCTACCGCATCGACCTAG 60.082 63.158 0.00 0.00 35.30 3.02
49 50 2.549198 CCGCTACCGCATCGACCTA 61.549 63.158 0.00 0.00 35.30 3.08
50 51 3.900892 CCGCTACCGCATCGACCT 61.901 66.667 0.00 0.00 35.30 3.85
52 53 4.865761 TGCCGCTACCGCATCGAC 62.866 66.667 0.00 0.00 35.30 4.20
53 54 3.439513 ATTGCCGCTACCGCATCGA 62.440 57.895 0.00 0.00 35.30 3.59
54 55 2.967076 ATTGCCGCTACCGCATCG 60.967 61.111 0.00 0.00 35.30 3.84
55 56 2.633657 CATTGCCGCTACCGCATC 59.366 61.111 0.00 0.00 35.30 3.91
56 57 3.585990 GCATTGCCGCTACCGCAT 61.586 61.111 0.00 0.00 35.30 4.73
67 68 0.749454 CTACACCTCCCTGGCATTGC 60.749 60.000 0.00 0.00 40.22 3.56
68 69 0.107017 CCTACACCTCCCTGGCATTG 60.107 60.000 0.00 0.00 40.22 2.82
69 70 0.253160 TCCTACACCTCCCTGGCATT 60.253 55.000 0.00 0.00 40.22 3.56
70 71 0.983378 GTCCTACACCTCCCTGGCAT 60.983 60.000 0.00 0.00 40.22 4.40
71 72 1.612442 GTCCTACACCTCCCTGGCA 60.612 63.158 0.00 0.00 40.22 4.92
72 73 2.722201 CGTCCTACACCTCCCTGGC 61.722 68.421 0.00 0.00 40.22 4.85
73 74 2.722201 GCGTCCTACACCTCCCTGG 61.722 68.421 0.00 0.00 42.93 4.45
74 75 1.949847 CTGCGTCCTACACCTCCCTG 61.950 65.000 0.00 0.00 0.00 4.45
75 76 1.682684 CTGCGTCCTACACCTCCCT 60.683 63.158 0.00 0.00 0.00 4.20
76 77 2.893398 CTGCGTCCTACACCTCCC 59.107 66.667 0.00 0.00 0.00 4.30
77 78 2.184579 GCTGCGTCCTACACCTCC 59.815 66.667 0.00 0.00 0.00 4.30
78 79 1.961180 ATGGCTGCGTCCTACACCTC 61.961 60.000 0.00 0.00 0.00 3.85
79 80 1.961180 GATGGCTGCGTCCTACACCT 61.961 60.000 0.00 0.00 0.00 4.00
80 81 1.521681 GATGGCTGCGTCCTACACC 60.522 63.158 0.00 0.00 0.00 4.16
81 82 1.521681 GGATGGCTGCGTCCTACAC 60.522 63.158 13.50 0.00 0.00 2.90
82 83 2.900273 GGATGGCTGCGTCCTACA 59.100 61.111 13.50 0.00 0.00 2.74
83 84 2.279517 CGGATGGCTGCGTCCTAC 60.280 66.667 17.11 0.00 32.19 3.18
84 85 4.221422 GCGGATGGCTGCGTCCTA 62.221 66.667 17.11 0.00 38.63 2.94
90 91 2.825387 TCATGTGCGGATGGCTGC 60.825 61.111 0.00 0.00 46.82 5.25
91 92 2.184830 CCTCATGTGCGGATGGCTG 61.185 63.158 0.00 0.00 44.05 4.85
92 93 2.191375 CCTCATGTGCGGATGGCT 59.809 61.111 0.00 0.00 44.05 4.75
93 94 2.324014 TACCCTCATGTGCGGATGGC 62.324 60.000 8.66 0.00 43.96 4.40
94 95 0.397941 ATACCCTCATGTGCGGATGG 59.602 55.000 8.66 0.00 0.00 3.51
95 96 1.516161 CATACCCTCATGTGCGGATG 58.484 55.000 8.66 0.73 0.00 3.51
96 97 0.250467 GCATACCCTCATGTGCGGAT 60.250 55.000 8.66 0.00 0.00 4.18
97 98 1.146041 GCATACCCTCATGTGCGGA 59.854 57.895 8.66 0.00 0.00 5.54
98 99 3.736483 GCATACCCTCATGTGCGG 58.264 61.111 0.00 0.00 0.00 5.69
100 101 2.546494 GCCGCATACCCTCATGTGC 61.546 63.158 0.00 0.00 35.52 4.57
101 102 2.246739 CGCCGCATACCCTCATGTG 61.247 63.158 0.00 0.00 36.40 3.21
102 103 2.108976 CGCCGCATACCCTCATGT 59.891 61.111 0.00 0.00 0.00 3.21
103 104 2.666190 CCGCCGCATACCCTCATG 60.666 66.667 0.00 0.00 0.00 3.07
104 105 3.941188 CCCGCCGCATACCCTCAT 61.941 66.667 0.00 0.00 0.00 2.90
115 116 3.113979 GTTTACACGTCCCCGCCG 61.114 66.667 0.00 0.00 37.70 6.46
116 117 3.113979 CGTTTACACGTCCCCGCC 61.114 66.667 0.00 0.00 41.84 6.13
125 126 1.123756 GCAGCACTACGTCGTTTACAC 59.876 52.381 1.78 0.00 0.00 2.90
126 127 1.001048 AGCAGCACTACGTCGTTTACA 60.001 47.619 1.78 0.00 0.00 2.41
127 128 1.647702 GAGCAGCACTACGTCGTTTAC 59.352 52.381 1.78 0.00 0.00 2.01
128 129 1.726892 CGAGCAGCACTACGTCGTTTA 60.727 52.381 1.78 0.00 0.00 2.01
129 130 1.002250 CGAGCAGCACTACGTCGTTT 61.002 55.000 1.78 0.00 0.00 3.60
130 131 1.442184 CGAGCAGCACTACGTCGTT 60.442 57.895 1.78 0.00 0.00 3.85
131 132 2.176055 CGAGCAGCACTACGTCGT 59.824 61.111 2.21 2.21 0.00 4.34
150 151 0.026803 GTCCGTCGTCGTATAACGCT 59.973 55.000 0.71 0.00 42.21 5.07
152 153 1.446731 GTGTCCGTCGTCGTATAACG 58.553 55.000 0.71 0.00 44.19 3.18
154 155 0.373370 CCGTGTCCGTCGTCGTATAA 59.627 55.000 0.71 0.00 35.01 0.98
157 158 2.664851 ACCGTGTCCGTCGTCGTA 60.665 61.111 0.71 0.00 35.01 3.43
158 159 4.318021 CACCGTGTCCGTCGTCGT 62.318 66.667 0.71 0.00 35.01 4.34
173 174 3.740128 ATGTCGATGCCCGGCTCAC 62.740 63.158 11.61 2.53 44.53 3.51
174 175 3.469970 ATGTCGATGCCCGGCTCA 61.470 61.111 11.61 0.00 44.53 4.26
235 236 2.981302 CACCATCGTCCAGAGCCA 59.019 61.111 0.00 0.00 0.00 4.75
240 241 1.812922 GCTCAGCACCATCGTCCAG 60.813 63.158 0.00 0.00 0.00 3.86
251 252 3.268965 GAGACGTCGTGGCTCAGCA 62.269 63.158 10.46 0.00 0.00 4.41
297 298 3.851128 GCTAGGTGGGGAGGACGC 61.851 72.222 0.00 0.00 0.00 5.19
300 301 2.365635 GCTGCTAGGTGGGGAGGA 60.366 66.667 0.00 0.00 0.00 3.71
306 307 1.220206 CCTGTGAGCTGCTAGGTGG 59.780 63.158 0.15 0.00 0.00 4.61
308 309 1.759445 CATACCTGTGAGCTGCTAGGT 59.241 52.381 22.36 22.36 45.11 3.08
316 317 1.745115 TTGCGGCATACCTGTGAGC 60.745 57.895 2.28 0.00 0.00 4.26
320 321 2.040544 GCAGTTGCGGCATACCTGT 61.041 57.895 19.37 0.53 0.00 4.00
365 366 2.119801 AGGGCATGTCATGACACTTC 57.880 50.000 30.09 20.03 45.05 3.01
391 392 4.111016 CGCCCTACACGACGCTGA 62.111 66.667 0.00 0.00 0.00 4.26
415 416 1.210478 AGACGGTGATGGATTTCAGGG 59.790 52.381 0.00 0.00 0.00 4.45
418 419 1.822371 TCGAGACGGTGATGGATTTCA 59.178 47.619 0.00 0.00 0.00 2.69
423 424 0.455815 CATGTCGAGACGGTGATGGA 59.544 55.000 0.00 0.00 0.00 3.41
433 434 2.095461 CTCCTGAAGACCATGTCGAGA 58.905 52.381 0.00 0.00 37.67 4.04
444 445 3.077556 GCGCCTCCCTCCTGAAGA 61.078 66.667 0.00 0.00 0.00 2.87
445 446 4.521062 CGCGCCTCCCTCCTGAAG 62.521 72.222 0.00 0.00 0.00 3.02
464 465 0.936764 CGCCGTGAGTAGCATAGCTG 60.937 60.000 0.00 0.00 40.10 4.24
465 466 1.101635 TCGCCGTGAGTAGCATAGCT 61.102 55.000 0.00 0.00 43.41 3.32
496 497 4.849329 CGTCGCGGCTACCACCTC 62.849 72.222 9.90 0.00 0.00 3.85
540 541 2.363925 GACCACCCTACCTCCGCT 60.364 66.667 0.00 0.00 0.00 5.52
557 558 3.011517 CACCCACCTCCTCCCTGG 61.012 72.222 0.00 0.00 37.10 4.45
619 625 5.184096 TGCACACTGACTTGGTAAAAGAAAA 59.816 36.000 0.00 0.00 0.00 2.29
633 639 0.599558 ATGTGGCATTGCACACTGAC 59.400 50.000 22.33 0.00 38.39 3.51
664 677 5.294060 TGGTTTTGTCTTTAACCGTACTGAC 59.706 40.000 0.00 0.00 45.40 3.51
689 702 6.659242 GGAGAGGTTTTGGACATAATTTGAGA 59.341 38.462 0.00 0.00 0.00 3.27
714 727 6.915349 TGTAAAACTGGATAAATGTTTCCCG 58.085 36.000 0.00 0.00 33.45 5.14
721 734 8.834465 CCTCAGATCTGTAAAACTGGATAAATG 58.166 37.037 21.92 0.00 0.00 2.32
812 836 2.171237 TGTCCATGGGCAACTATCTGAG 59.829 50.000 18.92 0.00 34.29 3.35
822 846 3.510559 TTGCAGCTGTCCATGGGCA 62.511 57.895 20.07 20.07 0.00 5.36
826 853 2.029739 TCAAATGTTGCAGCTGTCCATG 60.030 45.455 16.64 6.15 0.00 3.66
913 1858 0.039618 GGATCCACCTGGGCTTTTCA 59.960 55.000 6.95 0.00 36.21 2.69
991 1936 4.989168 GGTGTGTAATTTCTCTGTCGAGTT 59.011 41.667 0.00 0.00 38.45 3.01
1193 2139 5.163163 CCCAAGTAATTCATGGATCTGAGGA 60.163 44.000 5.82 0.00 37.10 3.71
1204 2150 4.569719 ACGGAAGTCCCAAGTAATTCAT 57.430 40.909 0.00 0.00 44.19 2.57
1222 2168 4.760665 ATCGAGCAGCAACGATCTACGG 62.761 54.545 17.69 0.00 44.14 4.02
1251 2197 2.417339 TCAGTCGAACTCCGTCAAAG 57.583 50.000 0.00 0.00 39.75 2.77
1284 2230 1.906574 AGGCTTCACCGGAATCACTAA 59.093 47.619 9.46 0.00 46.52 2.24
1343 2289 2.428544 ACAGAGCAGAGAGTACGGAT 57.571 50.000 0.00 0.00 0.00 4.18
1346 2292 3.308595 CAGACTACAGAGCAGAGAGTACG 59.691 52.174 0.00 0.00 0.00 3.67
1354 2300 1.403914 CCAGTGCAGACTACAGAGCAG 60.404 57.143 0.00 0.00 37.72 4.24
1356 2302 0.891373 TCCAGTGCAGACTACAGAGC 59.109 55.000 0.00 0.00 0.00 4.09
1357 2303 2.166829 ACTCCAGTGCAGACTACAGAG 58.833 52.381 0.00 0.00 32.80 3.35
1362 2308 4.515361 GACTACTACTCCAGTGCAGACTA 58.485 47.826 0.00 0.00 38.24 2.59
1364 2310 2.424246 GGACTACTACTCCAGTGCAGAC 59.576 54.545 0.00 0.00 38.24 3.51
1366 2312 1.402259 CGGACTACTACTCCAGTGCAG 59.598 57.143 0.00 0.00 38.24 4.41
1367 2313 1.271762 ACGGACTACTACTCCAGTGCA 60.272 52.381 0.00 0.00 38.24 4.57
1368 2314 1.132643 CACGGACTACTACTCCAGTGC 59.867 57.143 0.00 0.00 38.24 4.40
1369 2315 2.434428 ACACGGACTACTACTCCAGTG 58.566 52.381 0.00 0.00 38.24 3.66
1370 2316 2.875094 ACACGGACTACTACTCCAGT 57.125 50.000 0.00 0.00 41.62 4.00
1390 2336 4.084013 GCTTTCGAAAAAGAGACGGAATGA 60.084 41.667 12.41 0.00 43.90 2.57
1522 2468 2.223711 ACAAAACTAAACAAGGCAGCGG 60.224 45.455 0.00 0.00 0.00 5.52
1578 2524 8.149647 ACATGTGGTTCAACAAATGTAATTCAT 58.850 29.630 0.00 0.00 45.15 2.57
1610 2556 4.134563 ACATCCAGAAACACACCTTGTAC 58.865 43.478 0.00 0.00 37.51 2.90
1679 2625 5.242838 TCCTCGAACACAAAATGGCTAAATT 59.757 36.000 0.00 0.00 0.00 1.82
1694 2640 4.079970 ACAGATGAACTAGTCCTCGAACA 58.920 43.478 0.00 0.00 0.00 3.18
2076 3054 4.099573 ACGGAGGGAGTAGTTATCAATGTG 59.900 45.833 0.00 0.00 0.00 3.21
2228 3313 5.510671 AGATGCAGAAAACAGTTTGTAACG 58.489 37.500 0.00 0.00 36.23 3.18
2778 3868 9.281371 ACAATAATAGTACATAGCTGTCGTCTA 57.719 33.333 0.00 0.00 36.79 2.59
2900 3990 1.308998 CTGGACTGGGTTGTGACAAC 58.691 55.000 19.59 19.59 0.00 3.32
2975 4065 9.553064 CTTCACTAAGCAATGGAGACTATTATT 57.447 33.333 0.00 0.00 0.00 1.40
3321 4422 5.345702 CATGAAGTGTGCCCATGATTTTAG 58.654 41.667 0.00 0.00 39.86 1.85
3466 4567 6.708885 ATGACCCATATGTATTCCACTCAT 57.291 37.500 1.24 0.00 0.00 2.90
3868 4969 7.093596 CCTCTAGATGCCTTTTTCTCCATTTTT 60.094 37.037 0.00 0.00 0.00 1.94
4171 5272 5.986135 ACTCAGTCTCAAATGTGTCACTAAC 59.014 40.000 4.27 0.00 0.00 2.34
4210 5311 5.751028 CCTCGAAATGACAAGATTCTCTACC 59.249 44.000 0.00 0.00 0.00 3.18
4211 5312 5.233263 GCCTCGAAATGACAAGATTCTCTAC 59.767 44.000 0.00 0.00 0.00 2.59
4217 5322 4.954092 GAAGCCTCGAAATGACAAGATT 57.046 40.909 0.00 0.00 0.00 2.40
4232 5337 2.851195 ACAAAGACAACATCGAAGCCT 58.149 42.857 0.00 0.00 0.00 4.58
4241 5346 6.671614 ATGAAGTTCGTAACAAAGACAACA 57.328 33.333 0.00 0.00 0.00 3.33
4242 5347 8.280497 ACATATGAAGTTCGTAACAAAGACAAC 58.720 33.333 10.38 0.00 0.00 3.32
4261 5366 5.439721 AGCTATCACAAAGGCAACATATGA 58.560 37.500 10.38 0.00 41.41 2.15
4346 5451 4.162320 TCAGGCCTCGATTTAGTTCAAGAT 59.838 41.667 0.00 0.00 0.00 2.40
4518 5630 7.553881 AAGTATTCCATCCGTTCACAAATAG 57.446 36.000 0.00 0.00 0.00 1.73
4617 5729 3.424962 GGTTTCTGAATAGCACGCTGAAC 60.425 47.826 0.72 0.00 0.00 3.18
4628 5740 7.654022 ACTTTTGAAAGTGGGTTTCTGAATA 57.346 32.000 8.24 0.00 46.80 1.75
4666 5778 2.546584 GGCTTGCAGAAAACCTTTGGAG 60.547 50.000 0.00 0.00 0.00 3.86
4691 5803 9.461312 TGAAATACCAAAGCAGTTGATAGTTAT 57.539 29.630 1.93 0.00 39.87 1.89
4693 5805 7.448469 AGTGAAATACCAAAGCAGTTGATAGTT 59.552 33.333 1.93 0.00 39.87 2.24
4808 5920 2.279069 CCGAGTGTCTCCAGTGCCT 61.279 63.158 0.00 0.00 0.00 4.75
4809 5921 2.262915 CCGAGTGTCTCCAGTGCC 59.737 66.667 0.00 0.00 0.00 5.01
4814 5926 1.666011 GTTCTGCCGAGTGTCTCCA 59.334 57.895 0.00 0.00 0.00 3.86
4845 5957 2.046314 ATCGTGCCGGGGTTTCTG 60.046 61.111 2.18 0.00 0.00 3.02
5040 6152 1.446792 CGTCTACACCTGGCTGCTG 60.447 63.158 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.