Multiple sequence alignment - TraesCS5B01G184300

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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 TraesCS5B01G184300 chr5B 100.000 3410 0 0 1 3410 335200614 335204023 0.000000e+00 6298.0
1 TraesCS5B01G184300 chr5A 92.250 2955 171 36 5 2918 386696943 386699880 0.000000e+00 4135.0
2 TraesCS5B01G184300 chr5A 91.239 468 24 3 2948 3410 386699874 386700329 3.740000e-174 621.0
3 TraesCS5B01G184300 chr5D 96.473 2410 66 11 746 3147 293656773 293659171 0.000000e+00 3962.0
4 TraesCS5B01G184300 chr5D 85.866 658 75 10 5 644 293654834 293655491 0.000000e+00 684.0
5 TraesCS5B01G184300 chr5D 95.154 227 8 2 3185 3410 293659170 293659394 4.190000e-94 355.0
6 TraesCS5B01G184300 chr5D 80.258 233 38 5 465 691 251938174 251937944 5.850000e-38 169.0
7 TraesCS5B01G184300 chr5D 95.455 44 2 0 243 286 547453625 547453668 1.700000e-08 71.3
8 TraesCS5B01G184300 chr2A 79.874 318 48 10 417 727 16619978 16619670 5.730000e-53 219.0
9 TraesCS5B01G184300 chr2A 79.365 315 48 10 417 724 16605527 16605223 4.460000e-49 206.0
10 TraesCS5B01G184300 chr7A 80.657 274 45 6 418 690 708350845 708350579 4.460000e-49 206.0
11 TraesCS5B01G184300 chr7A 78.698 169 27 6 242 401 162114016 162113848 1.670000e-18 104.0
12 TraesCS5B01G184300 chr7D 76.168 428 67 17 2 395 396101999 396102425 3.470000e-45 193.0
13 TraesCS5B01G184300 chr7D 83.140 172 21 4 513 677 606799693 606799863 2.120000e-32 150.0
14 TraesCS5B01G184300 chr2D 84.516 155 21 3 533 685 61795779 61795932 2.120000e-32 150.0
15 TraesCS5B01G184300 chr2D 77.489 231 45 4 419 643 24224275 24224046 7.680000e-27 132.0
16 TraesCS5B01G184300 chr2D 82.576 132 16 3 445 571 89870578 89870707 3.600000e-20 110.0
17 TraesCS5B01G184300 chr7B 77.959 245 43 5 443 678 621296512 621296754 3.550000e-30 143.0
18 TraesCS5B01G184300 chr1D 82.099 162 20 5 244 404 401284698 401284851 2.760000e-26 130.0
19 TraesCS5B01G184300 chr4D 79.058 191 31 7 445 628 390609316 390609504 4.620000e-24 122.0
20 TraesCS5B01G184300 chr3B 79.651 172 23 4 242 401 429306642 429306471 2.780000e-21 113.0
21 TraesCS5B01G184300 chr6A 78.146 151 26 4 5 151 558816858 558817005 4.690000e-14 89.8
22 TraesCS5B01G184300 chr1B 88.889 63 6 1 243 304 176119370 176119432 3.650000e-10 76.8


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 TraesCS5B01G184300 chr5B 335200614 335204023 3409 False 6298 6298 100.000000 1 3410 1 chr5B.!!$F1 3409
1 TraesCS5B01G184300 chr5A 386696943 386700329 3386 False 2378 4135 91.744500 5 3410 2 chr5A.!!$F1 3405
2 TraesCS5B01G184300 chr5D 293654834 293659394 4560 False 1667 3962 92.497667 5 3410 3 chr5D.!!$F2 3405

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
699 750 0.034896 ACGGCCGGCTTCCATATTAG 59.965 55.0 31.76 7.34 0.0 1.73 F
730 1210 0.174845 GGATGTGATGTCCGGTCGAA 59.825 55.0 0.00 0.00 0.0 3.71 F
1989 3215 0.392998 CGAATTGGTGGGAGAGGGTG 60.393 60.0 0.00 0.00 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 3587 0.453390 CCAAATTCTTCGGAGCAGCC 59.547 55.000 0.0 0.0 0.0 4.85 R
2377 3603 2.306847 GTTCAAAGCTTCCCAGACCAA 58.693 47.619 0.0 0.0 0.0 3.67 R
3173 4439 0.674534 GTAGCATGGGTAGTCTCCGG 59.325 60.000 0.0 0.0 0.0 5.14 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
36 37 3.716195 CCATGGGTGAGGCCGTGA 61.716 66.667 2.85 0.00 38.44 4.35
44 45 0.525668 GTGAGGCCGTGATCACTACG 60.526 60.000 22.95 10.53 42.06 3.51
71 72 3.936203 TGTTGGAAGAGCGGCGGT 61.936 61.111 13.08 13.08 0.00 5.68
75 76 4.083862 GGAAGAGCGGCGGTCCTT 62.084 66.667 32.58 24.79 0.00 3.36
80 81 3.591254 GAGCGGCGGTCCTTGTTCT 62.591 63.158 27.28 2.35 0.00 3.01
83 84 1.153628 CGGCGGTCCTTGTTCTAGG 60.154 63.158 0.00 0.00 36.59 3.02
133 134 1.002868 CCTCCCTGACAAGCACCAG 60.003 63.158 0.00 0.00 0.00 4.00
134 135 1.673665 CTCCCTGACAAGCACCAGC 60.674 63.158 0.00 0.00 42.56 4.85
153 154 4.421479 CGCGGAGGAGCAACTCGT 62.421 66.667 0.00 0.00 38.39 4.18
154 155 2.048127 GCGGAGGAGCAACTCGTT 60.048 61.111 2.17 0.00 38.39 3.85
156 157 1.006102 CGGAGGAGCAACTCGTTGT 60.006 57.895 11.05 0.00 42.31 3.32
159 160 1.006102 AGGAGCAACTCGTTGTCGG 60.006 57.895 11.05 0.00 42.31 4.79
160 161 2.668280 GGAGCAACTCGTTGTCGGC 61.668 63.158 11.05 0.00 42.31 5.54
185 186 1.018752 CATTGCGTCGGATGTGGACA 61.019 55.000 0.00 0.00 34.04 4.02
227 229 3.622060 AATCCTTCCACACCGCCCG 62.622 63.158 0.00 0.00 0.00 6.13
231 233 3.605749 CTTCCACACCGCCCGTGAT 62.606 63.158 5.63 0.00 46.20 3.06
236 239 2.061578 ACACCGCCCGTGATATCCA 61.062 57.895 5.63 0.00 46.20 3.41
265 268 0.329596 AAGCCGCCTTCAAGGAGATT 59.670 50.000 7.98 0.00 37.36 2.40
290 294 1.141019 GCGGCGGATGAAGTCTACA 59.859 57.895 9.78 0.00 0.00 2.74
291 295 0.872021 GCGGCGGATGAAGTCTACAG 60.872 60.000 9.78 0.00 0.00 2.74
315 325 3.190849 CGAGGACGACGTCGCCTA 61.191 66.667 36.52 0.00 44.81 3.93
327 337 4.208686 CGCCTACTCCTCCACGCC 62.209 72.222 0.00 0.00 0.00 5.68
419 434 2.501223 TAGCTTGGTGGGCTTCGTCG 62.501 60.000 0.00 0.00 40.74 5.12
476 491 1.005332 TCATTTTTCGGGGCTCATGGA 59.995 47.619 0.00 0.00 0.00 3.41
478 493 0.958382 TTTTTCGGGGCTCATGGACG 60.958 55.000 0.00 0.00 0.00 4.79
501 516 1.408127 CCGATATGGGAAACAGGTGCA 60.408 52.381 0.00 0.00 0.00 4.57
508 523 1.230324 GGAAACAGGTGCAGACAGTC 58.770 55.000 0.00 0.00 0.00 3.51
530 545 8.475639 CAGTCATTTTAGGCTAGGTTTAGAGTA 58.524 37.037 0.00 0.00 0.00 2.59
649 700 7.327275 TGTTCAATTTCATTAAATTTCGACCGG 59.673 33.333 0.00 0.00 41.50 5.28
656 707 4.974368 TTAAATTTCGACCGGATGCAAT 57.026 36.364 9.46 0.00 0.00 3.56
681 732 4.379499 GGACATGTGTGGCTAGCTTTAAAC 60.379 45.833 15.72 7.52 32.35 2.01
686 737 1.022451 TGGCTAGCTTTAAACGGCCG 61.022 55.000 26.86 26.86 42.11 6.13
697 748 0.395173 AAACGGCCGGCTTCCATATT 60.395 50.000 31.76 8.20 0.00 1.28
699 750 0.034896 ACGGCCGGCTTCCATATTAG 59.965 55.000 31.76 7.34 0.00 1.73
705 756 3.804036 CCGGCTTCCATATTAGTGTTCA 58.196 45.455 0.00 0.00 0.00 3.18
708 759 4.319766 CGGCTTCCATATTAGTGTTCATGC 60.320 45.833 0.00 0.00 0.00 4.06
710 761 5.506317 GGCTTCCATATTAGTGTTCATGCAC 60.506 44.000 0.00 0.00 39.51 4.57
711 762 5.733226 TTCCATATTAGTGTTCATGCACG 57.267 39.130 0.00 0.00 43.61 5.34
716 767 2.760634 TAGTGTTCATGCACGGATGT 57.239 45.000 0.00 0.00 43.61 3.06
730 1210 0.174845 GGATGTGATGTCCGGTCGAA 59.825 55.000 0.00 0.00 0.00 3.71
733 1213 1.182667 TGTGATGTCCGGTCGAAGAT 58.817 50.000 0.00 0.00 40.67 2.40
738 1218 2.363795 TCCGGTCGAAGATGCCCT 60.364 61.111 0.00 0.00 40.67 5.19
750 1962 1.061812 AGATGCCCTAGGTGTGGATCT 60.062 52.381 12.72 12.72 0.00 2.75
754 1966 1.879575 CCCTAGGTGTGGATCTGGAA 58.120 55.000 8.29 0.00 0.00 3.53
755 1967 1.765314 CCCTAGGTGTGGATCTGGAAG 59.235 57.143 8.29 0.00 0.00 3.46
766 1978 0.962356 ATCTGGAAGCGTGGCAAAGG 60.962 55.000 0.00 0.00 0.00 3.11
895 2113 0.774908 CCCACCCTCCCTAACAAACA 59.225 55.000 0.00 0.00 0.00 2.83
896 2114 1.146152 CCCACCCTCCCTAACAAACAA 59.854 52.381 0.00 0.00 0.00 2.83
897 2115 2.425102 CCCACCCTCCCTAACAAACAAA 60.425 50.000 0.00 0.00 0.00 2.83
898 2116 2.626266 CCACCCTCCCTAACAAACAAAC 59.374 50.000 0.00 0.00 0.00 2.93
899 2117 2.626266 CACCCTCCCTAACAAACAAACC 59.374 50.000 0.00 0.00 0.00 3.27
900 2118 2.516702 ACCCTCCCTAACAAACAAACCT 59.483 45.455 0.00 0.00 0.00 3.50
1314 2540 2.341101 CCGCCTCACCGACTACACT 61.341 63.158 0.00 0.00 0.00 3.55
1884 3110 3.006859 AGTCAATCGTGTTCCTGATCACA 59.993 43.478 8.58 0.00 34.66 3.58
1929 3155 2.125512 GAGATCGCCGGTGTTGCT 60.126 61.111 16.01 10.63 0.00 3.91
1959 3185 1.684450 GTTTGGTACCCCTTGTTGGTG 59.316 52.381 10.07 0.00 36.57 4.17
1989 3215 0.392998 CGAATTGGTGGGAGAGGGTG 60.393 60.000 0.00 0.00 0.00 4.61
2061 3287 1.699083 TGCCTGAACCACTTCTCATCA 59.301 47.619 0.00 0.00 0.00 3.07
2067 3293 0.687354 ACCACTTCTCATCAGCCGTT 59.313 50.000 0.00 0.00 0.00 4.44
2115 3341 4.569279 TTTGAGAGGCAAACCGCA 57.431 50.000 0.00 0.00 45.17 5.69
2223 3449 0.755327 TGCCTCGCTGCCACTATAGA 60.755 55.000 6.78 0.00 0.00 1.98
2232 3458 1.760029 TGCCACTATAGAATGGTCGCA 59.240 47.619 6.78 0.00 35.73 5.10
2323 3549 4.430007 TGTAATGACATGGAAGACGCTAC 58.570 43.478 0.00 0.00 0.00 3.58
2361 3587 1.604378 CAGGGAAGCCACTACTGGG 59.396 63.158 0.00 0.00 38.13 4.45
2377 3603 1.077429 GGGGCTGCTCCGAAGAATT 60.077 57.895 1.06 0.00 34.94 2.17
2415 3641 0.914644 ACACTCATGGATGACTGGGG 59.085 55.000 4.37 0.00 32.50 4.96
2442 3668 3.873952 GGACTGGAGTATGAGACAATTGC 59.126 47.826 5.05 0.00 0.00 3.56
2443 3669 4.383552 GGACTGGAGTATGAGACAATTGCT 60.384 45.833 5.05 3.61 0.00 3.91
2571 3797 6.006449 AGGTGACTATCTTTGCAGTTCAATT 58.994 36.000 0.00 0.00 40.61 2.32
2576 3802 5.769662 ACTATCTTTGCAGTTCAATTGTGGA 59.230 36.000 5.13 0.00 34.12 4.02
2760 3987 6.838198 TTGATGGTTTGTAGCGTGTATATC 57.162 37.500 0.00 0.00 0.00 1.63
2761 3988 5.294356 TGATGGTTTGTAGCGTGTATATCC 58.706 41.667 0.00 0.00 0.00 2.59
2920 4186 9.912634 TTCTTTGTATTTTCTTTTAGGCATCTG 57.087 29.630 0.00 0.00 0.00 2.90
2921 4187 9.077885 TCTTTGTATTTTCTTTTAGGCATCTGT 57.922 29.630 0.00 0.00 0.00 3.41
2928 4194 9.657419 ATTTTCTTTTAGGCATCTGTAAAATGG 57.343 29.630 0.00 0.00 29.90 3.16
2929 4195 6.207691 TCTTTTAGGCATCTGTAAAATGGC 57.792 37.500 1.78 1.78 46.82 4.40
2932 4198 2.877043 GGCATCTGTAAAATGGCTGG 57.123 50.000 2.76 0.00 44.04 4.85
2933 4199 2.102578 GGCATCTGTAAAATGGCTGGT 58.897 47.619 2.76 0.00 44.04 4.00
2934 4200 2.497273 GGCATCTGTAAAATGGCTGGTT 59.503 45.455 2.76 0.00 44.04 3.67
2935 4201 3.699038 GGCATCTGTAAAATGGCTGGTTA 59.301 43.478 2.76 0.00 44.04 2.85
2936 4202 4.159506 GGCATCTGTAAAATGGCTGGTTAA 59.840 41.667 2.76 0.00 44.04 2.01
2937 4203 5.337169 GGCATCTGTAAAATGGCTGGTTAAA 60.337 40.000 2.76 0.00 44.04 1.52
2938 4204 6.162777 GCATCTGTAAAATGGCTGGTTAAAA 58.837 36.000 0.00 0.00 0.00 1.52
2939 4205 6.818142 GCATCTGTAAAATGGCTGGTTAAAAT 59.182 34.615 0.00 0.00 0.00 1.82
2940 4206 7.978975 GCATCTGTAAAATGGCTGGTTAAAATA 59.021 33.333 0.00 0.00 0.00 1.40
2941 4207 9.520204 CATCTGTAAAATGGCTGGTTAAAATAG 57.480 33.333 0.00 0.00 0.00 1.73
2942 4208 7.543756 TCTGTAAAATGGCTGGTTAAAATAGC 58.456 34.615 0.00 0.00 36.74 2.97
2943 4209 7.396055 TCTGTAAAATGGCTGGTTAAAATAGCT 59.604 33.333 0.00 0.00 37.58 3.32
2944 4210 7.543756 TGTAAAATGGCTGGTTAAAATAGCTC 58.456 34.615 0.00 0.00 37.58 4.09
2945 4211 6.603940 AAAATGGCTGGTTAAAATAGCTCA 57.396 33.333 0.00 0.00 37.58 4.26
2946 4212 5.582689 AATGGCTGGTTAAAATAGCTCAC 57.417 39.130 0.00 0.00 37.58 3.51
2947 4213 4.027674 TGGCTGGTTAAAATAGCTCACA 57.972 40.909 0.00 0.00 37.58 3.58
2995 4261 9.155975 GATTCTGCTATTTCTGAAGAGTTGTTA 57.844 33.333 0.00 0.00 0.00 2.41
3010 4276 7.907214 AGAGTTGTTAAATTGTTCTCGCTAT 57.093 32.000 0.00 0.00 0.00 2.97
3014 4280 8.730680 AGTTGTTAAATTGTTCTCGCTATGATT 58.269 29.630 0.00 0.00 0.00 2.57
3042 4308 7.661437 AGCTTTCAGATTTATGAACAGTGTGTA 59.339 33.333 0.00 0.00 38.87 2.90
3043 4309 8.454106 GCTTTCAGATTTATGAACAGTGTGTAT 58.546 33.333 0.00 0.00 38.87 2.29
3063 4329 3.808466 TTATGCTGCCTAGAGACTGTG 57.192 47.619 0.00 0.00 0.00 3.66
3074 4340 4.404073 CCTAGAGACTGTGTAGCTGGATTT 59.596 45.833 0.00 0.00 0.00 2.17
3146 4412 5.822519 TCTGCATACCATAAGTTCACAATCC 59.177 40.000 0.00 0.00 0.00 3.01
3166 4432 4.371786 TCCGTAGCATCATTTGTCTCATC 58.628 43.478 0.00 0.00 0.00 2.92
3173 4439 4.030977 GCATCATTTGTCTCATCGCAAAAC 59.969 41.667 0.00 0.00 37.98 2.43
3179 4445 0.606096 TCTCATCGCAAAACCGGAGA 59.394 50.000 9.46 0.00 0.00 3.71
3196 4466 2.362717 GGAGACTACCCATGCTACTGTC 59.637 54.545 0.00 0.00 0.00 3.51
3209 4479 3.260632 TGCTACTGTCCTTGCATAACTGA 59.739 43.478 0.00 0.00 0.00 3.41
3213 4483 4.655963 ACTGTCCTTGCATAACTGATGTT 58.344 39.130 0.00 0.00 37.90 2.71
3318 4589 0.733150 GTTTCCTGGCCACTAATCGC 59.267 55.000 0.00 0.00 0.00 4.58
3379 4650 4.501400 CCATTTCTTTGGTGTCTTTGTCCC 60.501 45.833 0.00 0.00 31.74 4.46
3382 4653 4.715534 TCTTTGGTGTCTTTGTCCCATA 57.284 40.909 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.807226 CGTAGTGATCACGGCCTCA 59.193 57.895 19.85 0.00 35.78 3.86
36 37 0.385751 CACCATCTCGGCGTAGTGAT 59.614 55.000 6.85 4.30 39.03 3.06
44 45 0.036388 TCTTCCAACACCATCTCGGC 60.036 55.000 0.00 0.00 39.03 5.54
71 72 3.309296 CCTATGCCTCCTAGAACAAGGA 58.691 50.000 0.00 0.00 43.58 3.36
140 141 1.009389 CCGACAACGAGTTGCTCCTC 61.009 60.000 15.09 5.30 44.03 3.71
169 170 1.447663 CATGTCCACATCCGACGCA 60.448 57.895 0.00 0.00 33.61 5.24
227 229 2.787601 TCTAACGCGGTGGATATCAC 57.212 50.000 5.94 1.21 45.34 3.06
231 233 0.103572 GGCTTCTAACGCGGTGGATA 59.896 55.000 12.18 1.50 0.00 2.59
268 271 4.514577 ACTTCATCCGCCGCCTCG 62.515 66.667 0.00 0.00 0.00 4.63
290 294 2.963371 GTCGTCCTCGTCCTTGCT 59.037 61.111 0.00 0.00 38.33 3.91
291 295 2.504244 CGTCGTCCTCGTCCTTGC 60.504 66.667 0.00 0.00 38.33 4.01
327 337 4.007940 CGTTGTCGTGTTGGCGGG 62.008 66.667 0.00 0.00 0.00 6.13
331 341 1.206578 GGCATCGTTGTCGTGTTGG 59.793 57.895 0.00 0.00 38.33 3.77
333 343 1.841663 GCTGGCATCGTTGTCGTGTT 61.842 55.000 0.00 0.00 38.33 3.32
334 344 2.317609 GCTGGCATCGTTGTCGTGT 61.318 57.895 0.00 0.00 38.33 4.49
337 347 2.476051 GTGCTGGCATCGTTGTCG 59.524 61.111 0.00 0.00 38.55 4.35
373 383 0.257905 TGCTCTACTCTTCCCCGCTA 59.742 55.000 0.00 0.00 0.00 4.26
376 386 0.390860 CCATGCTCTACTCTTCCCCG 59.609 60.000 0.00 0.00 0.00 5.73
419 434 3.745912 GCCTACGGCTAATTGGCC 58.254 61.111 22.20 22.20 46.69 5.36
432 447 3.461773 GCCTCCGCAGTCTGCCTA 61.462 66.667 19.14 6.43 41.12 3.93
452 467 1.177401 GAGCCCCGAAAAATGAAGCT 58.823 50.000 0.00 0.00 0.00 3.74
498 513 3.423539 AGCCTAAAATGACTGTCTGCA 57.576 42.857 9.51 0.00 0.00 4.41
501 516 5.763876 AACCTAGCCTAAAATGACTGTCT 57.236 39.130 9.51 0.00 0.00 3.41
576 595 9.947433 AACCCGGACGATATTAATTCATATTTA 57.053 29.630 0.73 0.00 0.00 1.40
587 606 8.991026 CATATTTAAACAACCCGGACGATATTA 58.009 33.333 0.73 0.00 0.00 0.98
649 700 1.064505 CCACACATGTCCGATTGCATC 59.935 52.381 0.00 0.00 0.00 3.91
656 707 1.218047 GCTAGCCACACATGTCCGA 59.782 57.895 2.29 0.00 0.00 4.55
681 732 0.034896 ACTAATATGGAAGCCGGCCG 59.965 55.000 26.15 21.04 0.00 6.13
686 737 4.580167 TGCATGAACACTAATATGGAAGCC 59.420 41.667 0.00 0.00 0.00 4.35
697 748 2.028567 TCACATCCGTGCATGAACACTA 60.029 45.455 7.72 0.00 43.28 2.74
699 750 1.155889 TCACATCCGTGCATGAACAC 58.844 50.000 7.72 0.00 43.28 3.32
705 756 3.085208 GGACATCACATCCGTGCAT 57.915 52.632 0.00 0.00 43.28 3.96
711 762 0.174845 TTCGACCGGACATCACATCC 59.825 55.000 9.46 0.00 0.00 3.51
716 767 0.179111 GCATCTTCGACCGGACATCA 60.179 55.000 9.46 0.00 0.00 3.07
718 769 1.144057 GGCATCTTCGACCGGACAT 59.856 57.895 9.46 0.00 0.00 3.06
726 1206 0.824109 CACACCTAGGGCATCTTCGA 59.176 55.000 14.81 0.00 0.00 3.71
730 1210 1.061812 AGATCCACACCTAGGGCATCT 60.062 52.381 14.81 8.77 0.00 2.90
733 1213 0.982852 CCAGATCCACACCTAGGGCA 60.983 60.000 14.81 0.00 0.00 5.36
738 1218 0.824109 CGCTTCCAGATCCACACCTA 59.176 55.000 0.00 0.00 0.00 3.08
750 1962 2.597217 CCCTTTGCCACGCTTCCA 60.597 61.111 0.00 0.00 0.00 3.53
773 1985 1.442769 TCTGAAATTGGCTGAGCGAC 58.557 50.000 0.00 0.00 0.00 5.19
895 2113 4.784177 TCTTAAAACAGGAACGGAGGTTT 58.216 39.130 0.00 0.00 36.24 3.27
896 2114 4.426736 TCTTAAAACAGGAACGGAGGTT 57.573 40.909 0.00 0.00 39.63 3.50
897 2115 4.565028 GGATCTTAAAACAGGAACGGAGGT 60.565 45.833 0.00 0.00 0.00 3.85
898 2116 3.939592 GGATCTTAAAACAGGAACGGAGG 59.060 47.826 0.00 0.00 0.00 4.30
899 2117 3.617263 CGGATCTTAAAACAGGAACGGAG 59.383 47.826 0.00 0.00 0.00 4.63
900 2118 3.258872 TCGGATCTTAAAACAGGAACGGA 59.741 43.478 0.00 0.00 0.00 4.69
1303 2529 1.608627 GGGGGACAGTGTAGTCGGT 60.609 63.158 0.00 0.00 39.42 4.69
1884 3110 2.032981 CTGCCGCACCTTCTTTTGT 58.967 52.632 0.00 0.00 0.00 2.83
1923 3149 1.034838 AAACCCAGAACGCAGCAACA 61.035 50.000 0.00 0.00 0.00 3.33
1929 3155 0.535553 GGTACCAAACCCAGAACGCA 60.536 55.000 7.15 0.00 43.16 5.24
1959 3185 1.244019 ACCAATTCGGCAGGCAAGAC 61.244 55.000 0.00 0.00 39.03 3.01
2061 3287 1.075836 TGGCCCAACATAAACGGCT 59.924 52.632 0.00 0.00 41.35 5.52
2232 3458 1.066908 CAAAGGTCACGCACAATTGGT 59.933 47.619 10.83 0.00 0.00 3.67
2235 3461 0.743688 TGCAAAGGTCACGCACAATT 59.256 45.000 0.00 0.00 0.00 2.32
2262 3488 1.091771 CAGCACCATAAGACAGCCCG 61.092 60.000 0.00 0.00 0.00 6.13
2361 3587 0.453390 CCAAATTCTTCGGAGCAGCC 59.547 55.000 0.00 0.00 0.00 4.85
2377 3603 2.306847 GTTCAAAGCTTCCCAGACCAA 58.693 47.619 0.00 0.00 0.00 3.67
2415 3641 4.211125 TGTCTCATACTCCAGTCCTGATC 58.789 47.826 0.00 0.00 0.00 2.92
2442 3668 2.951745 CGCAAGGCTCGACGCTAG 60.952 66.667 6.78 0.00 39.13 3.42
2443 3669 3.744719 ACGCAAGGCTCGACGCTA 61.745 61.111 2.34 0.00 46.39 4.26
2571 3797 3.253921 CACAACTGAAGCATGAATCCACA 59.746 43.478 0.00 0.00 0.00 4.17
2576 3802 5.532406 ACAAGTACACAACTGAAGCATGAAT 59.468 36.000 0.00 0.00 38.88 2.57
2673 3900 4.505039 GGATGTAAAGATAAGCCACGGGAT 60.505 45.833 0.00 0.00 0.00 3.85
2674 3901 3.181458 GGATGTAAAGATAAGCCACGGGA 60.181 47.826 0.00 0.00 0.00 5.14
2675 3902 3.139077 GGATGTAAAGATAAGCCACGGG 58.861 50.000 0.00 0.00 0.00 5.28
2906 4137 5.951747 AGCCATTTTACAGATGCCTAAAAGA 59.048 36.000 0.00 0.00 0.00 2.52
2913 4179 2.102578 ACCAGCCATTTTACAGATGCC 58.897 47.619 0.00 0.00 0.00 4.40
2914 4180 3.874392 AACCAGCCATTTTACAGATGC 57.126 42.857 0.00 0.00 0.00 3.91
2915 4181 9.520204 CTATTTTAACCAGCCATTTTACAGATG 57.480 33.333 0.00 0.00 0.00 2.90
2916 4182 8.197439 GCTATTTTAACCAGCCATTTTACAGAT 58.803 33.333 0.00 0.00 0.00 2.90
2917 4183 7.396055 AGCTATTTTAACCAGCCATTTTACAGA 59.604 33.333 0.00 0.00 35.88 3.41
2918 4184 7.547227 AGCTATTTTAACCAGCCATTTTACAG 58.453 34.615 0.00 0.00 35.88 2.74
2919 4185 7.177568 TGAGCTATTTTAACCAGCCATTTTACA 59.822 33.333 0.00 0.00 35.88 2.41
2920 4186 7.488150 GTGAGCTATTTTAACCAGCCATTTTAC 59.512 37.037 0.00 0.00 35.88 2.01
2921 4187 7.177568 TGTGAGCTATTTTAACCAGCCATTTTA 59.822 33.333 0.00 0.00 35.88 1.52
2922 4188 6.014669 TGTGAGCTATTTTAACCAGCCATTTT 60.015 34.615 0.00 0.00 35.88 1.82
2923 4189 5.480073 TGTGAGCTATTTTAACCAGCCATTT 59.520 36.000 0.00 0.00 35.88 2.32
2924 4190 5.016173 TGTGAGCTATTTTAACCAGCCATT 58.984 37.500 0.00 0.00 35.88 3.16
2925 4191 4.599041 TGTGAGCTATTTTAACCAGCCAT 58.401 39.130 0.00 0.00 35.88 4.40
2926 4192 4.009675 CTGTGAGCTATTTTAACCAGCCA 58.990 43.478 0.00 0.00 35.88 4.75
2927 4193 3.378427 CCTGTGAGCTATTTTAACCAGCC 59.622 47.826 0.00 0.00 35.88 4.85
2928 4194 3.378427 CCCTGTGAGCTATTTTAACCAGC 59.622 47.826 0.00 0.00 35.49 4.85
2929 4195 3.378427 GCCCTGTGAGCTATTTTAACCAG 59.622 47.826 0.00 0.00 0.00 4.00
2930 4196 3.245087 TGCCCTGTGAGCTATTTTAACCA 60.245 43.478 0.00 0.00 0.00 3.67
2931 4197 3.352648 TGCCCTGTGAGCTATTTTAACC 58.647 45.455 0.00 0.00 0.00 2.85
2932 4198 5.588648 TGTATGCCCTGTGAGCTATTTTAAC 59.411 40.000 0.00 0.00 0.00 2.01
2933 4199 5.750524 TGTATGCCCTGTGAGCTATTTTAA 58.249 37.500 0.00 0.00 0.00 1.52
2934 4200 5.366482 TGTATGCCCTGTGAGCTATTTTA 57.634 39.130 0.00 0.00 0.00 1.52
2935 4201 4.235079 TGTATGCCCTGTGAGCTATTTT 57.765 40.909 0.00 0.00 0.00 1.82
2936 4202 3.931907 TGTATGCCCTGTGAGCTATTT 57.068 42.857 0.00 0.00 0.00 1.40
2937 4203 3.931907 TTGTATGCCCTGTGAGCTATT 57.068 42.857 0.00 0.00 0.00 1.73
2938 4204 3.054434 TGTTTGTATGCCCTGTGAGCTAT 60.054 43.478 0.00 0.00 0.00 2.97
2939 4205 2.304470 TGTTTGTATGCCCTGTGAGCTA 59.696 45.455 0.00 0.00 0.00 3.32
2940 4206 1.073763 TGTTTGTATGCCCTGTGAGCT 59.926 47.619 0.00 0.00 0.00 4.09
2941 4207 1.200020 GTGTTTGTATGCCCTGTGAGC 59.800 52.381 0.00 0.00 0.00 4.26
2942 4208 2.783135 AGTGTTTGTATGCCCTGTGAG 58.217 47.619 0.00 0.00 0.00 3.51
2943 4209 2.949177 AGTGTTTGTATGCCCTGTGA 57.051 45.000 0.00 0.00 0.00 3.58
2944 4210 4.943705 AGAATAGTGTTTGTATGCCCTGTG 59.056 41.667 0.00 0.00 0.00 3.66
2945 4211 5.179452 AGAATAGTGTTTGTATGCCCTGT 57.821 39.130 0.00 0.00 0.00 4.00
2946 4212 5.647658 TCAAGAATAGTGTTTGTATGCCCTG 59.352 40.000 0.00 0.00 0.00 4.45
2947 4213 5.815581 TCAAGAATAGTGTTTGTATGCCCT 58.184 37.500 0.00 0.00 0.00 5.19
2995 4261 7.559590 AGCTTAATCATAGCGAGAACAATTT 57.440 32.000 0.00 0.00 43.37 1.82
2999 4265 6.106003 TGAAAGCTTAATCATAGCGAGAACA 58.894 36.000 0.00 0.00 43.37 3.18
3014 4280 8.506437 CACACTGTTCATAAATCTGAAAGCTTA 58.494 33.333 0.00 0.00 36.92 3.09
3033 4299 3.634397 AGGCAGCATAATACACACTGT 57.366 42.857 0.00 0.00 0.00 3.55
3042 4308 3.708631 ACACAGTCTCTAGGCAGCATAAT 59.291 43.478 0.00 0.00 0.00 1.28
3043 4309 3.099905 ACACAGTCTCTAGGCAGCATAA 58.900 45.455 0.00 0.00 0.00 1.90
3063 4329 5.125417 TGAATTGTTAGGCAAATCCAGCTAC 59.875 40.000 0.00 0.00 40.91 3.58
3074 4340 8.635765 AGTATCTTTTCTTGAATTGTTAGGCA 57.364 30.769 0.00 0.00 0.00 4.75
3130 4396 4.188462 TGCTACGGATTGTGAACTTATGG 58.812 43.478 0.00 0.00 0.00 2.74
3146 4412 3.362401 GCGATGAGACAAATGATGCTACG 60.362 47.826 0.00 0.00 0.00 3.51
3166 4432 1.017701 GGGTAGTCTCCGGTTTTGCG 61.018 60.000 0.00 0.00 0.00 4.85
3173 4439 0.674534 GTAGCATGGGTAGTCTCCGG 59.325 60.000 0.00 0.00 0.00 5.14
3179 4445 2.501723 CAAGGACAGTAGCATGGGTAGT 59.498 50.000 0.00 0.00 0.00 2.73
3196 4466 9.289303 GTTTTATACAACATCAGTTATGCAAGG 57.711 33.333 0.00 0.00 39.39 3.61
3213 4483 8.582657 TTGCAAATTAGCCCTAGTTTTATACA 57.417 30.769 0.00 0.00 0.00 2.29
3318 4589 1.213733 CGCATGCTGATCAGGACTCG 61.214 60.000 23.89 21.53 0.00 4.18
3345 4616 4.996758 ACCAAAGAAATGGCTGTATTTTGC 59.003 37.500 0.00 0.00 44.75 3.68


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

AutoCloner maintained by Alex Coulton.