Multiple sequence alignment - TraesCS1B01G322400

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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 TraesCS1B01G322400 chr1B 100.000 3056 0 0 1 3056 547280812 547283867 0.000000e+00 5644.0
1 TraesCS1B01G322400 chr1B 92.308 299 17 3 1 299 130133419 130133711 1.310000e-113 420.0
2 TraesCS1B01G322400 chr1D 95.000 2440 71 25 513 2927 406972556 406974969 0.000000e+00 3783.0
3 TraesCS1B01G322400 chr1D 93.243 296 13 5 1 296 376863431 376863719 2.180000e-116 429.0
4 TraesCS1B01G322400 chr1D 81.466 232 20 13 290 515 406972306 406972520 5.240000e-38 169.0
5 TraesCS1B01G322400 chr1D 97.500 40 1 0 3017 3056 406975001 406975040 5.470000e-08 69.4
6 TraesCS1B01G322400 chr1A 94.123 2161 59 24 912 3037 502677635 502679762 0.000000e+00 3225.0
7 TraesCS1B01G322400 chr1A 95.960 297 6 3 1 296 480588771 480589062 7.670000e-131 477.0
8 TraesCS1B01G322400 chr1A 90.805 348 14 9 511 842 502676981 502677326 1.670000e-122 449.0
9 TraesCS1B01G322400 chr1A 83.190 232 14 16 290 515 502676733 502676945 4.020000e-44 189.0
10 TraesCS1B01G322400 chr3D 90.077 1038 98 5 1020 2054 437779397 437778362 0.000000e+00 1341.0
11 TraesCS1B01G322400 chr3B 89.583 1056 108 2 1020 2074 572936895 572935841 0.000000e+00 1339.0
12 TraesCS1B01G322400 chr3A 89.904 1040 98 7 1020 2054 575948971 575947934 0.000000e+00 1332.0
13 TraesCS1B01G322400 chr3A 96.959 296 4 1 1 296 704647241 704647531 2.740000e-135 492.0
14 TraesCS1B01G322400 chr3A 91.973 299 17 4 1 297 219342767 219342474 2.190000e-111 412.0
15 TraesCS1B01G322400 chr3A 91.722 302 18 4 1 300 334784788 334784492 2.190000e-111 412.0
16 TraesCS1B01G322400 chr5A 82.696 942 148 11 1043 1972 308376769 308375831 0.000000e+00 822.0
17 TraesCS1B01G322400 chr5D 82.150 958 154 12 1028 1972 243219947 243220900 0.000000e+00 806.0
18 TraesCS1B01G322400 chr5B 82.359 941 153 9 1043 1972 255200464 255199526 0.000000e+00 806.0
19 TraesCS1B01G322400 chr7A 92.977 299 12 6 1 296 575439174 575439466 7.830000e-116 427.0
20 TraesCS1B01G322400 chr4A 92.000 300 17 4 1 298 403171926 403172220 6.100000e-112 414.0
21 TraesCS1B01G322400 chr4D 91.946 298 16 5 4 298 112226154 112225862 7.890000e-111 411.0
22 TraesCS1B01G322400 chr7B 100.000 30 0 0 1289 1318 508981759 508981730 4.260000e-04 56.5


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 TraesCS1B01G322400 chr1B 547280812 547283867 3055 False 5644.000000 5644 100.000000 1 3056 1 chr1B.!!$F2 3055
1 TraesCS1B01G322400 chr1D 406972306 406975040 2734 False 1340.466667 3783 91.322000 290 3056 3 chr1D.!!$F2 2766
2 TraesCS1B01G322400 chr1A 502676733 502679762 3029 False 1287.666667 3225 89.372667 290 3037 3 chr1A.!!$F2 2747
3 TraesCS1B01G322400 chr3D 437778362 437779397 1035 True 1341.000000 1341 90.077000 1020 2054 1 chr3D.!!$R1 1034
4 TraesCS1B01G322400 chr3B 572935841 572936895 1054 True 1339.000000 1339 89.583000 1020 2074 1 chr3B.!!$R1 1054
5 TraesCS1B01G322400 chr3A 575947934 575948971 1037 True 1332.000000 1332 89.904000 1020 2054 1 chr3A.!!$R3 1034
6 TraesCS1B01G322400 chr5A 308375831 308376769 938 True 822.000000 822 82.696000 1043 1972 1 chr5A.!!$R1 929
7 TraesCS1B01G322400 chr5D 243219947 243220900 953 False 806.000000 806 82.150000 1028 1972 1 chr5D.!!$F1 944
8 TraesCS1B01G322400 chr5B 255199526 255200464 938 True 806.000000 806 82.359000 1043 1972 1 chr5B.!!$R1 929

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
408 415 0.251922 AGAACCATGCCATTGCCACT 60.252 50.000 0.0 0.0 36.33 4.00 F
515 524 1.068127 GTGTCACTCAACGGTAGGTGT 59.932 52.381 0.0 0.0 36.22 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1752 2.408271 TGTTGAGCATGGAGGATGAC 57.592 50.000 0.0 0.0 33.31 3.06 R
2414 2766 3.691118 GGAAGATGCATAGTGAGCAAACA 59.309 43.478 0.0 0.0 46.27 2.83 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
66 67 7.312415 ACGTAAAATATAGCCCAATAGGTCT 57.688 36.000 0.00 0.00 38.26 3.85
67 68 8.426569 ACGTAAAATATAGCCCAATAGGTCTA 57.573 34.615 0.00 0.00 38.26 2.59
68 69 8.873144 ACGTAAAATATAGCCCAATAGGTCTAA 58.127 33.333 0.00 0.00 38.26 2.10
69 70 9.715121 CGTAAAATATAGCCCAATAGGTCTAAA 57.285 33.333 0.00 0.00 38.26 1.85
73 74 8.935614 AATATAGCCCAATAGGTCTAAAAACC 57.064 34.615 0.00 0.00 39.80 3.27
74 75 4.668138 AGCCCAATAGGTCTAAAAACCA 57.332 40.909 0.00 0.00 42.12 3.67
75 76 4.600062 AGCCCAATAGGTCTAAAAACCAG 58.400 43.478 0.00 0.00 42.12 4.00
76 77 3.130516 GCCCAATAGGTCTAAAAACCAGC 59.869 47.826 0.00 0.00 42.12 4.85
77 78 3.699538 CCCAATAGGTCTAAAAACCAGCC 59.300 47.826 0.00 0.00 42.12 4.85
78 79 3.699538 CCAATAGGTCTAAAAACCAGCCC 59.300 47.826 0.00 0.00 42.12 5.19
79 80 4.340617 CAATAGGTCTAAAAACCAGCCCA 58.659 43.478 0.00 0.00 42.12 5.36
80 81 4.668138 ATAGGTCTAAAAACCAGCCCAA 57.332 40.909 0.00 0.00 42.12 4.12
81 82 2.594131 AGGTCTAAAAACCAGCCCAAC 58.406 47.619 0.00 0.00 42.12 3.77
82 83 2.091555 AGGTCTAAAAACCAGCCCAACA 60.092 45.455 0.00 0.00 42.12 3.33
83 84 2.296190 GGTCTAAAAACCAGCCCAACAG 59.704 50.000 0.00 0.00 39.27 3.16
84 85 2.296190 GTCTAAAAACCAGCCCAACAGG 59.704 50.000 0.00 0.00 39.47 4.00
85 86 1.618343 CTAAAAACCAGCCCAACAGGG 59.382 52.381 0.00 0.00 46.03 4.45
95 96 3.525268 GCCCAACAGGGTGAAAATATG 57.475 47.619 2.03 0.00 44.99 1.78
96 97 2.418609 GCCCAACAGGGTGAAAATATGC 60.419 50.000 2.03 0.00 44.99 3.14
97 98 2.830923 CCCAACAGGGTGAAAATATGCA 59.169 45.455 0.00 0.00 37.83 3.96
98 99 3.119029 CCCAACAGGGTGAAAATATGCAG 60.119 47.826 0.00 0.00 37.83 4.41
99 100 3.514645 CAACAGGGTGAAAATATGCAGC 58.485 45.455 0.00 0.00 0.00 5.25
102 103 1.484038 GGGTGAAAATATGCAGCCCA 58.516 50.000 9.42 0.00 44.68 5.36
103 104 1.410153 GGGTGAAAATATGCAGCCCAG 59.590 52.381 9.42 0.00 44.68 4.45
104 105 1.202452 GGTGAAAATATGCAGCCCAGC 60.202 52.381 0.00 0.00 0.00 4.85
105 106 0.740149 TGAAAATATGCAGCCCAGCG 59.260 50.000 0.00 0.00 37.31 5.18
106 107 0.740737 GAAAATATGCAGCCCAGCGT 59.259 50.000 0.00 0.00 37.31 5.07
107 108 0.457035 AAAATATGCAGCCCAGCGTG 59.543 50.000 0.00 0.00 37.31 5.34
108 109 2.008268 AAATATGCAGCCCAGCGTGC 62.008 55.000 0.00 4.69 40.29 5.34
109 110 2.898920 AATATGCAGCCCAGCGTGCT 62.899 55.000 0.00 0.00 40.54 4.40
110 111 2.043604 ATATGCAGCCCAGCGTGCTA 62.044 55.000 0.00 4.06 40.54 3.49
111 112 2.250741 TATGCAGCCCAGCGTGCTAA 62.251 55.000 0.00 0.00 40.54 3.09
112 113 3.055719 GCAGCCCAGCGTGCTAAA 61.056 61.111 0.00 0.00 36.81 1.85
113 114 2.870372 CAGCCCAGCGTGCTAAAC 59.130 61.111 0.00 0.00 36.81 2.01
124 125 1.283736 GTGCTAAACGTACCATCGGG 58.716 55.000 0.00 0.00 41.29 5.14
125 126 0.460635 TGCTAAACGTACCATCGGGC 60.461 55.000 0.00 0.00 37.90 6.13
126 127 1.156034 GCTAAACGTACCATCGGGCC 61.156 60.000 0.00 0.00 37.90 5.80
127 128 0.872881 CTAAACGTACCATCGGGCCG 60.873 60.000 22.51 22.51 37.90 6.13
128 129 2.295472 TAAACGTACCATCGGGCCGG 62.295 60.000 27.98 13.02 36.46 6.13
140 141 2.268600 GGCCGGCCCGTTTACTAA 59.731 61.111 36.64 0.00 0.00 2.24
141 142 1.153107 GGCCGGCCCGTTTACTAAT 60.153 57.895 36.64 0.00 0.00 1.73
142 143 1.162181 GGCCGGCCCGTTTACTAATC 61.162 60.000 36.64 4.14 0.00 1.75
143 144 0.462403 GCCGGCCCGTTTACTAATCA 60.462 55.000 18.11 0.00 0.00 2.57
144 145 1.578583 CCGGCCCGTTTACTAATCAG 58.421 55.000 0.85 0.00 0.00 2.90
145 146 1.578583 CGGCCCGTTTACTAATCAGG 58.421 55.000 0.00 0.00 0.00 3.86
146 147 1.306148 GGCCCGTTTACTAATCAGGC 58.694 55.000 0.00 0.00 38.21 4.85
147 148 1.306148 GCCCGTTTACTAATCAGGCC 58.694 55.000 0.00 0.00 32.68 5.19
148 149 1.578583 CCCGTTTACTAATCAGGCCG 58.421 55.000 0.00 0.00 0.00 6.13
149 150 1.134610 CCCGTTTACTAATCAGGCCGT 60.135 52.381 0.00 0.00 0.00 5.68
150 151 1.931172 CCGTTTACTAATCAGGCCGTG 59.069 52.381 0.00 0.00 0.00 4.94
151 152 1.326548 CGTTTACTAATCAGGCCGTGC 59.673 52.381 0.00 0.00 0.00 5.34
163 164 3.399181 CCGTGCCTGGGCTAAGGA 61.399 66.667 13.05 0.00 40.02 3.36
164 165 2.187946 CGTGCCTGGGCTAAGGAG 59.812 66.667 13.05 0.00 40.02 3.69
174 175 4.148825 CTAAGGAGCTGCGCCCGT 62.149 66.667 19.12 12.50 0.00 5.28
175 176 4.451150 TAAGGAGCTGCGCCCGTG 62.451 66.667 19.12 0.00 0.00 4.94
202 203 4.244463 GGCACGGCCCGGCTATTA 62.244 66.667 8.57 0.00 44.06 0.98
203 204 2.203098 GCACGGCCCGGCTATTAA 60.203 61.111 8.57 0.00 0.00 1.40
204 205 1.820481 GCACGGCCCGGCTATTAAA 60.820 57.895 8.57 0.00 0.00 1.52
205 206 2.019337 CACGGCCCGGCTATTAAAC 58.981 57.895 8.57 0.00 0.00 2.01
206 207 1.522130 ACGGCCCGGCTATTAAACG 60.522 57.895 8.57 4.87 0.00 3.60
207 208 1.522130 CGGCCCGGCTATTAAACGT 60.522 57.895 9.86 0.00 0.00 3.99
208 209 1.768112 CGGCCCGGCTATTAAACGTG 61.768 60.000 9.86 0.00 0.00 4.49
209 210 1.354155 GCCCGGCTATTAAACGTGC 59.646 57.895 0.71 0.00 0.00 5.34
210 211 2.019337 CCCGGCTATTAAACGTGCC 58.981 57.895 0.00 2.35 41.76 5.01
211 212 0.745128 CCCGGCTATTAAACGTGCCA 60.745 55.000 12.24 0.00 45.13 4.92
212 213 0.375803 CCGGCTATTAAACGTGCCAC 59.624 55.000 12.24 0.00 45.13 5.01
243 244 2.902343 GGGCCAGGCACGATTAGC 60.902 66.667 15.19 0.00 0.00 3.09
244 245 2.124736 GGCCAGGCACGATTAGCA 60.125 61.111 15.19 0.00 0.00 3.49
245 246 2.472909 GGCCAGGCACGATTAGCAC 61.473 63.158 15.19 0.00 0.00 4.40
246 247 1.745115 GCCAGGCACGATTAGCACA 60.745 57.895 6.55 0.00 0.00 4.57
247 248 1.709147 GCCAGGCACGATTAGCACAG 61.709 60.000 6.55 0.00 0.00 3.66
248 249 1.091771 CCAGGCACGATTAGCACAGG 61.092 60.000 0.00 0.00 0.00 4.00
249 250 1.450312 AGGCACGATTAGCACAGGC 60.450 57.895 0.00 0.00 41.61 4.85
250 251 2.472909 GGCACGATTAGCACAGGCC 61.473 63.158 0.00 0.00 42.56 5.19
251 252 2.813179 GCACGATTAGCACAGGCCG 61.813 63.158 0.00 0.00 42.56 6.13
252 253 1.447838 CACGATTAGCACAGGCCGT 60.448 57.895 0.00 0.00 42.56 5.68
314 315 1.689813 TGCTCTTAAGTCGGTCAACCA 59.310 47.619 1.63 0.00 35.14 3.67
320 321 2.922740 AAGTCGGTCAACCAGCTTAA 57.077 45.000 0.00 0.00 35.14 1.85
408 415 0.251922 AGAACCATGCCATTGCCACT 60.252 50.000 0.00 0.00 36.33 4.00
425 432 3.535561 CCACTCCATGACACCAACTATC 58.464 50.000 0.00 0.00 0.00 2.08
427 434 4.186926 CACTCCATGACACCAACTATCTG 58.813 47.826 0.00 0.00 0.00 2.90
428 435 4.081476 CACTCCATGACACCAACTATCTGA 60.081 45.833 0.00 0.00 0.00 3.27
430 437 5.190528 ACTCCATGACACCAACTATCTGATT 59.809 40.000 0.00 0.00 0.00 2.57
431 438 5.674525 TCCATGACACCAACTATCTGATTC 58.325 41.667 0.00 0.00 0.00 2.52
461 470 9.736414 TTTACTACTAATACATCTAGGCGATCT 57.264 33.333 0.00 0.00 0.00 2.75
464 473 9.332502 ACTACTAATACATCTAGGCGATCTATG 57.667 37.037 0.00 0.00 0.00 2.23
474 483 7.619512 TCTAGGCGATCTATGATCTATCCTA 57.380 40.000 6.09 10.78 0.00 2.94
480 489 7.201866 GGCGATCTATGATCTATCCTAACACAT 60.202 40.741 6.09 0.00 0.00 3.21
515 524 1.068127 GTGTCACTCAACGGTAGGTGT 59.932 52.381 0.00 0.00 36.22 4.16
572 621 1.877443 ACCCATGACAGTACAAAACGC 59.123 47.619 0.00 0.00 0.00 4.84
573 622 1.876799 CCCATGACAGTACAAAACGCA 59.123 47.619 0.00 0.00 0.00 5.24
590 639 2.364002 ACGCAGGCACTTTTTAAACCAT 59.636 40.909 0.00 0.00 34.60 3.55
722 783 6.183360 GGAAAGAAGGAAAGAAAAGGAAAGCT 60.183 38.462 0.00 0.00 0.00 3.74
725 786 8.484214 AAGAAGGAAAGAAAAGGAAAGCTATT 57.516 30.769 0.00 0.00 0.00 1.73
727 788 7.507277 AGAAGGAAAGAAAAGGAAAGCTATTGT 59.493 33.333 0.00 0.00 0.00 2.71
773 834 2.124570 CAAGCACCCATCCCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
792 853 1.221021 CCCTCGCCTCACCTAAACC 59.779 63.158 0.00 0.00 0.00 3.27
2162 2501 8.915654 CACAATAGGCTTGTTATTTTTCTTGAC 58.084 33.333 0.00 0.00 0.00 3.18
2211 2551 6.380560 TGGAGAAATGTATGATTCATTGGCAA 59.619 34.615 0.68 0.68 35.95 4.52
2242 2582 1.135689 GCGATGTACTTTGCCCACTTG 60.136 52.381 9.38 0.00 0.00 3.16
2243 2583 2.151202 CGATGTACTTTGCCCACTTGT 58.849 47.619 0.00 0.00 0.00 3.16
2244 2584 2.095768 CGATGTACTTTGCCCACTTGTG 60.096 50.000 0.00 0.00 0.00 3.33
2245 2585 2.428544 TGTACTTTGCCCACTTGTGT 57.571 45.000 0.00 0.00 0.00 3.72
2246 2586 2.729194 TGTACTTTGCCCACTTGTGTT 58.271 42.857 0.00 0.00 0.00 3.32
2247 2587 2.685897 TGTACTTTGCCCACTTGTGTTC 59.314 45.455 0.00 0.00 0.00 3.18
2248 2588 2.143876 ACTTTGCCCACTTGTGTTCT 57.856 45.000 0.00 0.00 0.00 3.01
2254 2594 2.094286 TGCCCACTTGTGTTCTTTGTTG 60.094 45.455 0.00 0.00 0.00 3.33
2292 2635 5.349061 AAAGATCAATGGGGATGCTTTTC 57.651 39.130 0.00 0.00 28.94 2.29
2311 2654 4.481930 TTCCACAATTAAGTTGCTGTCG 57.518 40.909 0.00 0.00 41.69 4.35
2329 2672 5.390567 GCTGTCGTTCTACTTTTTATGGTGG 60.391 44.000 0.00 0.00 0.00 4.61
2411 2763 7.657761 AGAAACATGAGAGTACTCGAAATTGTT 59.342 33.333 17.07 17.94 45.25 2.83
2414 2766 9.436957 AACATGAGAGTACTCGAAATTGTTATT 57.563 29.630 17.07 0.00 45.25 1.40
2572 2924 7.792364 TTAACTTTAGTTGGATCTGAGGAGA 57.208 36.000 5.41 0.00 38.90 3.71
2843 3195 9.555727 TGTAAACTATATTCAATAGTTGCCTCC 57.444 33.333 10.32 0.84 42.19 4.30
2860 3212 8.055790 AGTTGCCTCCTTTAGCTTTTAATATCT 58.944 33.333 0.00 0.00 0.00 1.98
2891 3243 2.287909 GCTTCGGTTTGTTGCATGGTTA 60.288 45.455 0.00 0.00 0.00 2.85
2912 3264 6.016777 GGTTAGGTGAATATTTGCCTGATCAG 60.017 42.308 16.24 16.24 32.90 2.90
2925 3277 3.743521 CCTGATCAGTTTTCACCTGACA 58.256 45.455 21.11 0.00 41.47 3.58
3016 3371 3.922850 GTCACTAGGTGCGGTAACTTAAC 59.077 47.826 0.00 0.00 32.98 2.01
3017 3372 3.828451 TCACTAGGTGCGGTAACTTAACT 59.172 43.478 0.00 0.00 32.98 2.24
3018 3373 4.281688 TCACTAGGTGCGGTAACTTAACTT 59.718 41.667 0.00 0.00 32.98 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.130516 GCTGGTTTTTAGACCTATTGGGC 59.869 47.826 0.00 0.00 43.41 5.36
55 56 3.699538 GGCTGGTTTTTAGACCTATTGGG 59.300 47.826 0.00 0.00 40.47 4.12
56 57 3.699538 GGGCTGGTTTTTAGACCTATTGG 59.300 47.826 0.00 0.00 40.38 3.16
57 58 4.340617 TGGGCTGGTTTTTAGACCTATTG 58.659 43.478 0.00 0.00 44.11 1.90
58 59 4.668138 TGGGCTGGTTTTTAGACCTATT 57.332 40.909 0.00 0.00 44.11 1.73
59 60 4.202631 TGTTGGGCTGGTTTTTAGACCTAT 60.203 41.667 0.00 0.00 44.11 2.57
60 61 3.138653 TGTTGGGCTGGTTTTTAGACCTA 59.861 43.478 0.00 0.00 44.11 3.08
61 62 2.091555 TGTTGGGCTGGTTTTTAGACCT 60.092 45.455 0.00 0.00 44.11 3.85
62 63 2.296190 CTGTTGGGCTGGTTTTTAGACC 59.704 50.000 0.00 0.00 44.04 3.85
63 64 2.296190 CCTGTTGGGCTGGTTTTTAGAC 59.704 50.000 0.00 0.00 0.00 2.59
64 65 2.593026 CCTGTTGGGCTGGTTTTTAGA 58.407 47.619 0.00 0.00 0.00 2.10
77 78 3.676873 GCTGCATATTTTCACCCTGTTGG 60.677 47.826 0.00 0.00 41.37 3.77
78 79 3.514645 GCTGCATATTTTCACCCTGTTG 58.485 45.455 0.00 0.00 0.00 3.33
79 80 2.497273 GGCTGCATATTTTCACCCTGTT 59.503 45.455 0.50 0.00 0.00 3.16
80 81 2.102578 GGCTGCATATTTTCACCCTGT 58.897 47.619 0.50 0.00 0.00 4.00
81 82 1.410153 GGGCTGCATATTTTCACCCTG 59.590 52.381 0.50 0.00 32.88 4.45
82 83 1.006998 TGGGCTGCATATTTTCACCCT 59.993 47.619 0.50 0.00 36.78 4.34
83 84 1.410153 CTGGGCTGCATATTTTCACCC 59.590 52.381 0.50 0.00 36.36 4.61
84 85 1.202452 GCTGGGCTGCATATTTTCACC 60.202 52.381 0.50 0.00 0.00 4.02
85 86 1.534595 CGCTGGGCTGCATATTTTCAC 60.535 52.381 0.50 0.00 0.00 3.18
86 87 0.740149 CGCTGGGCTGCATATTTTCA 59.260 50.000 0.50 0.00 0.00 2.69
87 88 0.740737 ACGCTGGGCTGCATATTTTC 59.259 50.000 0.50 0.00 0.00 2.29
88 89 0.457035 CACGCTGGGCTGCATATTTT 59.543 50.000 0.50 0.00 0.00 1.82
89 90 2.008268 GCACGCTGGGCTGCATATTT 62.008 55.000 0.50 0.00 34.58 1.40
90 91 2.484062 GCACGCTGGGCTGCATATT 61.484 57.895 0.50 0.00 34.58 1.28
91 92 2.043604 TAGCACGCTGGGCTGCATAT 62.044 55.000 14.30 4.45 42.62 1.78
92 93 2.250741 TTAGCACGCTGGGCTGCATA 62.251 55.000 14.30 0.00 42.62 3.14
93 94 3.626996 TTAGCACGCTGGGCTGCAT 62.627 57.895 14.30 8.26 42.62 3.96
94 95 3.841137 TTTAGCACGCTGGGCTGCA 62.841 57.895 14.30 0.00 42.62 4.41
95 96 3.055719 TTTAGCACGCTGGGCTGC 61.056 61.111 14.30 9.91 42.62 5.25
96 97 2.870372 GTTTAGCACGCTGGGCTG 59.130 61.111 14.30 0.00 42.62 4.85
97 98 2.742372 CGTTTAGCACGCTGGGCT 60.742 61.111 10.07 10.07 43.37 5.19
105 106 1.283736 CCCGATGGTACGTTTAGCAC 58.716 55.000 0.00 0.00 38.51 4.40
106 107 0.460635 GCCCGATGGTACGTTTAGCA 60.461 55.000 0.00 0.00 39.98 3.49
107 108 1.156034 GGCCCGATGGTACGTTTAGC 61.156 60.000 0.00 0.00 0.00 3.09
108 109 0.872881 CGGCCCGATGGTACGTTTAG 60.873 60.000 0.00 0.00 32.04 1.85
109 110 1.141449 CGGCCCGATGGTACGTTTA 59.859 57.895 0.00 0.00 32.04 2.01
110 111 2.125431 CGGCCCGATGGTACGTTT 60.125 61.111 0.00 0.00 32.04 3.60
111 112 4.151582 CCGGCCCGATGGTACGTT 62.152 66.667 3.71 0.00 33.93 3.99
123 124 1.153107 ATTAGTAAACGGGCCGGCC 60.153 57.895 38.57 38.57 0.00 6.13
124 125 0.462403 TGATTAGTAAACGGGCCGGC 60.462 55.000 31.78 21.18 0.00 6.13
125 126 1.578583 CTGATTAGTAAACGGGCCGG 58.421 55.000 31.78 12.53 0.00 6.13
126 127 1.578583 CCTGATTAGTAAACGGGCCG 58.421 55.000 27.06 27.06 0.00 6.13
127 128 1.306148 GCCTGATTAGTAAACGGGCC 58.694 55.000 25.41 12.20 46.61 5.80
129 130 1.134610 ACGGCCTGATTAGTAAACGGG 60.135 52.381 12.58 12.58 0.00 5.28
130 131 1.931172 CACGGCCTGATTAGTAAACGG 59.069 52.381 0.00 0.00 0.00 4.44
131 132 1.326548 GCACGGCCTGATTAGTAAACG 59.673 52.381 0.00 0.00 0.00 3.60
132 133 1.669265 GGCACGGCCTGATTAGTAAAC 59.331 52.381 0.00 0.00 46.69 2.01
133 134 2.032680 GGCACGGCCTGATTAGTAAA 57.967 50.000 0.00 0.00 46.69 2.01
134 135 3.772619 GGCACGGCCTGATTAGTAA 57.227 52.632 0.00 0.00 46.69 2.24
146 147 3.391665 CTCCTTAGCCCAGGCACGG 62.392 68.421 12.03 7.92 44.88 4.94
147 148 2.187946 CTCCTTAGCCCAGGCACG 59.812 66.667 12.03 0.00 44.88 5.34
148 149 2.124529 GCTCCTTAGCCCAGGCAC 60.125 66.667 12.03 0.00 43.40 5.01
186 187 1.820481 TTTAATAGCCGGGCCGTGC 60.820 57.895 26.32 25.86 0.00 5.34
187 188 1.768112 CGTTTAATAGCCGGGCCGTG 61.768 60.000 26.32 17.25 0.00 4.94
188 189 1.522130 CGTTTAATAGCCGGGCCGT 60.522 57.895 26.32 10.07 0.00 5.68
189 190 1.522130 ACGTTTAATAGCCGGGCCG 60.522 57.895 21.46 21.46 0.00 6.13
190 191 2.019337 CACGTTTAATAGCCGGGCC 58.981 57.895 17.02 0.00 0.00 5.80
191 192 1.354155 GCACGTTTAATAGCCGGGC 59.646 57.895 12.11 12.11 44.35 6.13
192 193 2.019337 GGCACGTTTAATAGCCGGG 58.981 57.895 2.18 0.00 37.41 5.73
196 197 0.247934 GCCGTGGCACGTTTAATAGC 60.248 55.000 34.74 25.38 40.58 2.97
197 198 0.025770 CGCCGTGGCACGTTTAATAG 59.974 55.000 34.74 20.30 40.58 1.73
198 199 1.360194 CCGCCGTGGCACGTTTAATA 61.360 55.000 34.74 0.00 40.58 0.98
199 200 2.682876 CCGCCGTGGCACGTTTAAT 61.683 57.895 34.74 0.00 40.58 1.40
200 201 3.347405 CCGCCGTGGCACGTTTAA 61.347 61.111 34.74 0.00 40.58 1.52
224 225 4.169696 TAATCGTGCCTGGCCCGG 62.170 66.667 22.84 9.24 0.00 5.73
225 226 2.588877 CTAATCGTGCCTGGCCCG 60.589 66.667 17.67 17.67 0.00 6.13
226 227 2.902343 GCTAATCGTGCCTGGCCC 60.902 66.667 17.53 2.94 0.00 5.80
227 228 2.124736 TGCTAATCGTGCCTGGCC 60.125 61.111 17.53 6.66 0.00 5.36
228 229 1.709147 CTGTGCTAATCGTGCCTGGC 61.709 60.000 12.87 12.87 0.00 4.85
229 230 1.091771 CCTGTGCTAATCGTGCCTGG 61.092 60.000 0.00 0.00 0.00 4.45
230 231 1.709147 GCCTGTGCTAATCGTGCCTG 61.709 60.000 0.00 0.00 33.53 4.85
231 232 1.450312 GCCTGTGCTAATCGTGCCT 60.450 57.895 0.00 0.00 33.53 4.75
232 233 2.472909 GGCCTGTGCTAATCGTGCC 61.473 63.158 0.00 0.00 37.74 5.01
233 234 2.813179 CGGCCTGTGCTAATCGTGC 61.813 63.158 0.00 0.00 37.74 5.34
234 235 1.447838 ACGGCCTGTGCTAATCGTG 60.448 57.895 0.00 0.00 37.74 4.35
235 236 1.447838 CACGGCCTGTGCTAATCGT 60.448 57.895 13.44 0.00 42.70 3.73
236 237 3.398920 CACGGCCTGTGCTAATCG 58.601 61.111 13.44 0.00 42.70 3.34
278 279 2.505982 CATACCTGGCCAGACGGG 59.494 66.667 34.91 20.85 42.81 5.28
279 280 2.203070 GCATACCTGGCCAGACGG 60.203 66.667 34.91 21.25 0.00 4.79
280 281 1.227380 GAGCATACCTGGCCAGACG 60.227 63.158 34.91 20.56 0.00 4.18
281 282 0.543749 AAGAGCATACCTGGCCAGAC 59.456 55.000 34.91 16.74 0.00 3.51
282 283 2.174685 TAAGAGCATACCTGGCCAGA 57.825 50.000 34.91 16.18 0.00 3.86
283 284 2.171448 ACTTAAGAGCATACCTGGCCAG 59.829 50.000 26.87 26.87 0.00 4.85
284 285 2.170607 GACTTAAGAGCATACCTGGCCA 59.829 50.000 10.09 4.71 0.00 5.36
285 286 2.803492 CGACTTAAGAGCATACCTGGCC 60.803 54.545 10.09 0.00 0.00 5.36
286 287 2.474816 CGACTTAAGAGCATACCTGGC 58.525 52.381 10.09 0.00 0.00 4.85
287 288 2.431057 ACCGACTTAAGAGCATACCTGG 59.569 50.000 10.09 0.00 0.00 4.45
288 289 3.130516 TGACCGACTTAAGAGCATACCTG 59.869 47.826 10.09 0.00 0.00 4.00
292 293 3.512329 TGGTTGACCGACTTAAGAGCATA 59.488 43.478 10.09 0.00 39.43 3.14
294 295 1.689813 TGGTTGACCGACTTAAGAGCA 59.310 47.619 10.09 0.00 39.43 4.26
344 351 0.040958 CACGAAGCTTCACCTGTTGC 60.041 55.000 25.47 0.00 0.00 4.17
348 355 1.597854 TGGCACGAAGCTTCACCTG 60.598 57.895 25.47 17.04 44.79 4.00
372 379 7.201609 GCATGGTTCTTACATCGATTTTCACTA 60.202 37.037 0.00 0.00 0.00 2.74
373 380 6.403636 GCATGGTTCTTACATCGATTTTCACT 60.404 38.462 0.00 0.00 0.00 3.41
408 415 5.426509 AGAATCAGATAGTTGGTGTCATGGA 59.573 40.000 0.00 0.00 0.00 3.41
445 454 9.448438 GATAGATCATAGATCGCCTAGATGTAT 57.552 37.037 0.00 0.00 43.94 2.29
446 455 7.880713 GGATAGATCATAGATCGCCTAGATGTA 59.119 40.741 0.00 0.00 40.26 2.29
447 456 6.714810 GGATAGATCATAGATCGCCTAGATGT 59.285 42.308 0.00 0.00 40.26 3.06
448 457 6.942005 AGGATAGATCATAGATCGCCTAGATG 59.058 42.308 13.53 0.00 40.26 2.90
449 458 7.090319 AGGATAGATCATAGATCGCCTAGAT 57.910 40.000 13.53 0.00 43.51 1.98
450 459 6.508030 AGGATAGATCATAGATCGCCTAGA 57.492 41.667 13.53 0.00 0.00 2.43
451 460 7.717436 TGTTAGGATAGATCATAGATCGCCTAG 59.283 40.741 17.36 0.00 0.00 3.02
452 461 7.499563 GTGTTAGGATAGATCATAGATCGCCTA 59.500 40.741 15.65 15.65 0.00 3.93
453 462 6.320164 GTGTTAGGATAGATCATAGATCGCCT 59.680 42.308 16.97 16.97 0.00 5.52
454 463 6.095580 TGTGTTAGGATAGATCATAGATCGCC 59.904 42.308 0.00 5.30 0.00 5.54
455 464 7.089770 TGTGTTAGGATAGATCATAGATCGC 57.910 40.000 0.00 0.00 0.00 4.58
456 465 7.647318 GCATGTGTTAGGATAGATCATAGATCG 59.353 40.741 0.00 0.00 0.00 3.69
457 466 7.647318 CGCATGTGTTAGGATAGATCATAGATC 59.353 40.741 0.00 0.00 0.00 2.75
458 467 7.417229 CCGCATGTGTTAGGATAGATCATAGAT 60.417 40.741 5.38 0.00 0.00 1.98
459 468 6.127619 CCGCATGTGTTAGGATAGATCATAGA 60.128 42.308 5.38 0.00 0.00 1.98
460 469 6.038985 CCGCATGTGTTAGGATAGATCATAG 58.961 44.000 5.38 0.00 0.00 2.23
461 470 5.624509 GCCGCATGTGTTAGGATAGATCATA 60.625 44.000 5.38 0.00 0.00 2.15
462 471 4.825422 CCGCATGTGTTAGGATAGATCAT 58.175 43.478 5.38 0.00 0.00 2.45
463 472 3.554960 GCCGCATGTGTTAGGATAGATCA 60.555 47.826 5.38 0.00 0.00 2.92
464 473 2.996621 GCCGCATGTGTTAGGATAGATC 59.003 50.000 5.38 0.00 0.00 2.75
474 483 0.523072 GTCAATGAGCCGCATGTGTT 59.477 50.000 5.38 0.00 37.28 3.32
495 504 1.068127 ACACCTACCGTTGAGTGACAC 59.932 52.381 0.00 0.00 34.33 3.67
572 621 3.980775 CGTGATGGTTTAAAAAGTGCCTG 59.019 43.478 0.00 0.00 0.00 4.85
573 622 3.634910 ACGTGATGGTTTAAAAAGTGCCT 59.365 39.130 0.00 0.00 0.00 4.75
694 748 3.305403 CCTTTTCTTTCCTTCTTTCCGCC 60.305 47.826 0.00 0.00 0.00 6.13
722 783 2.502130 TGGCCACGTGGAGAATACAATA 59.498 45.455 38.30 7.55 37.39 1.90
725 786 0.249120 CTGGCCACGTGGAGAATACA 59.751 55.000 38.30 21.83 37.39 2.29
727 788 1.220749 GCTGGCCACGTGGAGAATA 59.779 57.895 38.30 16.33 37.39 1.75
773 834 1.449778 GTTTAGGTGAGGCGAGGGC 60.450 63.158 0.00 0.00 38.90 5.19
844 910 0.536006 CGGATCTGAGGATTTGGGGC 60.536 60.000 0.00 0.00 31.46 5.80
886 952 4.452733 GACTTGGACTCGGGCGGG 62.453 72.222 0.00 0.00 0.00 6.13
887 953 4.452733 GGACTTGGACTCGGGCGG 62.453 72.222 0.00 0.00 0.00 6.13
888 954 3.691342 TGGACTTGGACTCGGGCG 61.691 66.667 0.00 0.00 0.00 6.13
889 955 2.047179 GTGGACTTGGACTCGGGC 60.047 66.667 0.00 0.00 0.00 6.13
896 962 2.204090 GGGAGGGGTGGACTTGGA 60.204 66.667 0.00 0.00 0.00 3.53
1423 1750 4.719286 ATGTTGAGCATGGAGGATGACCT 61.719 47.826 0.00 0.00 42.19 3.85
1425 1752 2.408271 TGTTGAGCATGGAGGATGAC 57.592 50.000 0.00 0.00 33.31 3.06
2162 2501 6.966534 ATTTTATTCCTCTACCATGGCAAG 57.033 37.500 13.04 10.16 0.00 4.01
2211 2551 6.136071 GCAAAGTACATCGCGATTTTCATAT 58.864 36.000 21.14 0.22 0.00 1.78
2292 2635 3.896648 ACGACAGCAACTTAATTGTGG 57.103 42.857 0.00 0.00 40.77 4.17
2311 2654 5.567430 AGTCCCCACCATAAAAAGTAGAAC 58.433 41.667 0.00 0.00 0.00 3.01
2329 2672 8.704849 AGCATGTAGATCTATATGATAGTCCC 57.295 38.462 32.19 17.96 36.98 4.46
2395 2747 8.015658 AGCAAACAATAACAATTTCGAGTACTC 58.984 33.333 13.18 13.18 0.00 2.59
2411 2763 6.038603 GGAAGATGCATAGTGAGCAAACAATA 59.961 38.462 0.00 0.00 46.27 1.90
2414 2766 3.691118 GGAAGATGCATAGTGAGCAAACA 59.309 43.478 0.00 0.00 46.27 2.83
2572 2924 5.683681 AGATCAACAAATTGCCTTGGTTTT 58.316 33.333 0.00 0.00 35.63 2.43
2860 3212 5.218885 CAACAAACCGAAGCATAATCACAA 58.781 37.500 0.00 0.00 0.00 3.33
2872 3224 2.294791 CCTAACCATGCAACAAACCGAA 59.705 45.455 0.00 0.00 0.00 4.30
2891 3243 5.121380 ACTGATCAGGCAAATATTCACCT 57.879 39.130 26.08 3.86 0.00 4.00
2912 3264 3.972502 GCAATACGTTGTCAGGTGAAAAC 59.027 43.478 0.00 3.26 38.57 2.43
2925 3277 9.988350 CATGTAAAAGAATCTTAGCAATACGTT 57.012 29.630 0.00 0.00 0.00 3.99
3016 3371 7.699391 CCTGAATACATGACAATGCAACTTAAG 59.301 37.037 0.00 0.00 37.29 1.85
3017 3372 7.176515 ACCTGAATACATGACAATGCAACTTAA 59.823 33.333 0.00 0.00 37.29 1.85
3018 3373 6.658816 ACCTGAATACATGACAATGCAACTTA 59.341 34.615 0.00 0.00 37.29 2.24


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

AutoCloner maintained by Alex Coulton.