Multiple sequence alignment - TraesCS3B01G408500

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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 TraesCS3B01G408500 chr3B 100.000 2717 0 0 1 2717 644164125 644161409 0.000000e+00 5018.0
1 TraesCS3B01G408500 chr3D 92.964 1606 76 20 337 1936 482185328 482183754 0.000000e+00 2305.0
2 TraesCS3B01G408500 chr3D 88.629 299 26 5 1 299 482185620 482185330 9.250000e-95 357.0
3 TraesCS3B01G408500 chr3D 86.364 176 15 6 410 584 482186596 482186429 1.660000e-42 183.0
4 TraesCS3B01G408500 chr3A 94.885 958 44 2 1056 2013 625200613 625199661 0.000000e+00 1493.0
5 TraesCS3B01G408500 chr3A 88.028 710 53 19 363 1061 625206626 625205938 0.000000e+00 811.0
6 TraesCS3B01G408500 chr3A 87.667 300 28 5 1 299 625206926 625206635 9.320000e-90 340.0
7 TraesCS3B01G408500 chr3A 89.172 157 14 3 2015 2169 625199566 625199411 2.760000e-45 193.0
8 TraesCS3B01G408500 chr2D 92.500 40 2 1 2156 2194 526114688 526114649 3.780000e-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 TraesCS3B01G408500 chr3B 644161409 644164125 2716 True 5018.000000 5018 100.0000 1 2717 1 chr3B.!!$R1 2716
1 TraesCS3B01G408500 chr3D 482183754 482186596 2842 True 948.333333 2305 89.3190 1 1936 3 chr3D.!!$R1 1935
2 TraesCS3B01G408500 chr3A 625199411 625200613 1202 True 843.000000 1493 92.0285 1056 2169 2 chr3A.!!$R1 1113
3 TraesCS3B01G408500 chr3A 625205938 625206926 988 True 575.500000 811 87.8475 1 1061 2 chr3A.!!$R2 1060

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
511 1490 0.366871 CGTCAGTAGCAACGATGTGC 59.633 55.0 0.0 0.0 45.28 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 3152 0.252012 TATGGCCAAGGGTGGGTTTG 60.252 55.0 10.96 0.0 46.09 2.93 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
30 1006 2.340210 TATGTATGGGCAATGCACGT 57.660 45.000 7.56 7.56 32.76 4.49
40 1016 4.340666 TGGGCAATGCACGTTTGATATTAT 59.659 37.500 7.79 0.00 32.76 1.28
60 1036 3.755965 TGCAGGTATTAATTGCACACG 57.244 42.857 8.83 0.00 42.41 4.49
124 1100 3.951037 AGCGGTGATGGCAATATTTGTTA 59.049 39.130 0.00 0.00 0.00 2.41
125 1101 4.036734 AGCGGTGATGGCAATATTTGTTAG 59.963 41.667 0.00 0.00 0.00 2.34
126 1102 4.290155 CGGTGATGGCAATATTTGTTAGC 58.710 43.478 0.00 0.00 0.00 3.09
182 1158 5.008019 CGCTCACCATTTGAAGCAATATAGT 59.992 40.000 0.00 0.00 32.21 2.12
183 1159 6.202762 CGCTCACCATTTGAAGCAATATAGTA 59.797 38.462 0.00 0.00 32.21 1.82
184 1160 7.570140 CGCTCACCATTTGAAGCAATATAGTAG 60.570 40.741 0.00 0.00 32.21 2.57
185 1161 7.308229 GCTCACCATTTGAAGCAATATAGTAGG 60.308 40.741 0.00 0.00 32.21 3.18
203 1180 3.146104 AGGTTGTTGGATTGACCTGAG 57.854 47.619 0.00 0.00 40.84 3.35
252 1229 8.600625 TCTACCATTTTGAATCTTTTCGTATCG 58.399 33.333 0.00 0.00 34.39 2.92
257 1234 5.524511 TTGAATCTTTTCGTATCGGTGTG 57.475 39.130 0.00 0.00 34.39 3.82
304 1281 9.640963 GTAGAGCTCTATTTAGAAGAACAAACA 57.359 33.333 25.74 0.00 0.00 2.83
306 1283 9.561069 AGAGCTCTATTTAGAAGAACAAACAAA 57.439 29.630 16.50 0.00 0.00 2.83
417 1395 8.422577 AAATATTCTCTTTACAAAAGCCACCT 57.577 30.769 0.00 0.00 0.00 4.00
479 1457 3.697542 CACAAGATTTGGCATGATCCTGA 59.302 43.478 13.66 0.00 34.12 3.86
498 1477 1.755393 AAGGGCGAAAGGACGTCAGT 61.755 55.000 18.91 0.02 39.76 3.41
511 1490 0.366871 CGTCAGTAGCAACGATGTGC 59.633 55.000 0.00 0.00 45.28 4.57
580 1559 5.173312 CGTGACGCTCAACCAAATATAGTAG 59.827 44.000 0.00 0.00 0.00 2.57
698 1677 5.665916 ATCAAAATCATCCTCACAAACCC 57.334 39.130 0.00 0.00 0.00 4.11
709 1688 3.307480 CCTCACAAACCCGTAAAGATCCT 60.307 47.826 0.00 0.00 0.00 3.24
780 1759 5.450453 TCCTCTCCTATCAAATCGTCTCTT 58.550 41.667 0.00 0.00 0.00 2.85
784 1763 5.069251 TCTCCTATCAAATCGTCTCTTTCCC 59.931 44.000 0.00 0.00 0.00 3.97
785 1764 4.962995 TCCTATCAAATCGTCTCTTTCCCT 59.037 41.667 0.00 0.00 0.00 4.20
809 1788 1.255859 CGTTGTTCGTAAGTCGCAACA 59.744 47.619 0.00 6.44 40.89 3.33
825 1804 2.723658 GCAACACGCGAAATTTCATCAA 59.276 40.909 15.93 0.00 0.00 2.57
828 1807 3.296628 ACACGCGAAATTTCATCAACAC 58.703 40.909 15.93 0.00 0.00 3.32
829 1808 2.656422 CACGCGAAATTTCATCAACACC 59.344 45.455 15.93 0.00 0.00 4.16
838 1817 8.333908 CGAAATTTCATCAACACCAAAAATCAA 58.666 29.630 17.99 0.00 0.00 2.57
844 1823 3.629855 TCAACACCAAAAATCAAGCGAGA 59.370 39.130 0.00 0.00 0.00 4.04
864 1843 4.999939 GCCCAAAGCAACCGCGTG 63.000 66.667 4.92 0.00 45.49 5.34
865 1844 3.283684 CCCAAAGCAACCGCGTGA 61.284 61.111 4.92 0.00 45.49 4.35
932 1911 1.449601 ACGATCGTTGGGCCATCAC 60.450 57.895 16.60 1.79 0.00 3.06
933 1912 2.525248 CGATCGTTGGGCCATCACG 61.525 63.158 21.72 21.72 0.00 4.35
934 1913 1.153449 GATCGTTGGGCCATCACGA 60.153 57.895 29.41 29.41 37.24 4.35
950 1933 0.948678 ACGAACCCATTTCACCAACG 59.051 50.000 0.00 0.00 33.24 4.10
978 1961 2.050269 CCTTCACGACCAGGTCACT 58.950 57.895 20.13 0.35 32.09 3.41
982 1965 1.531423 TCACGACCAGGTCACTAGTC 58.469 55.000 20.13 0.00 32.83 2.59
993 1976 2.897969 GGTCACTAGTCCAGTTCAGGAA 59.102 50.000 0.00 0.00 39.92 3.36
1176 2162 0.537188 TCTTCAAGGTCATCGCCCTC 59.463 55.000 0.00 0.00 0.00 4.30
1194 2180 2.969238 GTCATCATCGCGCTGGGG 60.969 66.667 10.42 2.88 0.00 4.96
1218 2204 2.925170 ACCCTCGTGCTCTGGCTT 60.925 61.111 0.00 0.00 39.59 4.35
1466 2452 4.537433 GAGGAAGGGCGAGCGCAT 62.537 66.667 17.16 1.99 44.11 4.73
1717 2703 3.112709 GCGCCGTGGACTTCTGAC 61.113 66.667 0.00 0.00 0.00 3.51
1930 2919 4.663636 AATTCGACACCTTGAATTCGTC 57.336 40.909 0.04 0.94 39.89 4.20
1964 2953 7.411049 CCGTATTATATTGCGAATTCGTGCTTA 60.411 37.037 27.24 14.86 42.22 3.09
1965 2954 7.947830 CGTATTATATTGCGAATTCGTGCTTAA 59.052 33.333 27.24 18.07 42.22 1.85
1966 2955 9.588774 GTATTATATTGCGAATTCGTGCTTAAA 57.411 29.630 27.24 15.93 42.22 1.52
1968 2957 9.677567 ATTATATTGCGAATTCGTGCTTAAATT 57.322 25.926 27.24 7.99 42.22 1.82
1969 2958 7.985634 ATATTGCGAATTCGTGCTTAAATTT 57.014 28.000 27.24 10.96 42.22 1.82
1970 2959 6.704512 ATTGCGAATTCGTGCTTAAATTTT 57.295 29.167 27.24 0.80 42.22 1.82
1971 2960 7.804614 ATTGCGAATTCGTGCTTAAATTTTA 57.195 28.000 27.24 0.00 42.22 1.52
2018 3007 4.098416 GGCAACATAAAAGAAGATCACGC 58.902 43.478 0.00 0.00 0.00 5.34
2021 3104 5.629020 GCAACATAAAAGAAGATCACGCAAA 59.371 36.000 0.00 0.00 0.00 3.68
2037 3120 7.706281 TCACGCAAAAACATTTCAAATATGT 57.294 28.000 0.00 0.00 37.82 2.29
2039 3122 8.060679 TCACGCAAAAACATTTCAAATATGTTG 58.939 29.630 0.00 0.00 43.44 3.33
2061 3145 4.398988 TGATGCAGCCAAAATAACTAGTGG 59.601 41.667 0.00 0.00 0.00 4.00
2062 3146 4.027674 TGCAGCCAAAATAACTAGTGGA 57.972 40.909 0.00 0.00 32.54 4.02
2067 3151 5.016173 AGCCAAAATAACTAGTGGATGCAA 58.984 37.500 0.00 0.00 32.54 4.08
2068 3152 5.102313 GCCAAAATAACTAGTGGATGCAAC 58.898 41.667 0.00 0.00 32.54 4.17
2072 3156 7.116233 CCAAAATAACTAGTGGATGCAACAAAC 59.884 37.037 0.00 0.00 32.54 2.93
2075 3159 2.158534 ACTAGTGGATGCAACAAACCCA 60.159 45.455 0.00 0.00 0.00 4.51
2078 3162 1.118356 TGGATGCAACAAACCCACCC 61.118 55.000 0.00 0.00 0.00 4.61
2091 3175 1.454479 CCACCCTTGGCCATAGCAG 60.454 63.158 6.09 0.00 42.56 4.24
2097 3181 1.224075 CTTGGCCATAGCAGATCACG 58.776 55.000 6.09 0.00 42.56 4.35
2100 3184 0.815213 GGCCATAGCAGATCACGCAA 60.815 55.000 0.00 0.00 42.56 4.85
2200 3284 9.793252 ATTTCTGAAATGAAAAATATCACCTCG 57.207 29.630 14.47 0.00 39.08 4.63
2201 3285 6.785191 TCTGAAATGAAAAATATCACCTCGC 58.215 36.000 0.00 0.00 30.82 5.03
2202 3286 6.374053 TCTGAAATGAAAAATATCACCTCGCA 59.626 34.615 0.00 0.00 30.82 5.10
2203 3287 6.918626 TGAAATGAAAAATATCACCTCGCAA 58.081 32.000 0.00 0.00 30.82 4.85
2204 3288 7.374272 TGAAATGAAAAATATCACCTCGCAAA 58.626 30.769 0.00 0.00 30.82 3.68
2205 3289 7.869937 TGAAATGAAAAATATCACCTCGCAAAA 59.130 29.630 0.00 0.00 30.82 2.44
2206 3290 8.600449 AAATGAAAAATATCACCTCGCAAAAA 57.400 26.923 0.00 0.00 30.82 1.94
2250 3334 9.596677 AATTTTAAAAATGTTCATCATGCGTTG 57.403 25.926 4.44 0.00 36.81 4.10
2251 3335 7.936950 TTTAAAAATGTTCATCATGCGTTGA 57.063 28.000 0.00 0.00 39.12 3.18
2252 3336 7.936950 TTAAAAATGTTCATCATGCGTTGAA 57.063 28.000 0.00 0.00 38.03 2.69
2253 3337 8.531622 TTAAAAATGTTCATCATGCGTTGAAT 57.468 26.923 8.25 0.00 38.03 2.57
2254 3338 9.631452 TTAAAAATGTTCATCATGCGTTGAATA 57.369 25.926 8.25 6.75 38.03 1.75
2255 3339 8.531622 AAAAATGTTCATCATGCGTTGAATAA 57.468 26.923 8.25 2.96 38.03 1.40
2256 3340 8.531622 AAAATGTTCATCATGCGTTGAATAAA 57.468 26.923 8.25 1.18 38.03 1.40
2257 3341 7.745022 AATGTTCATCATGCGTTGAATAAAG 57.255 32.000 8.25 0.00 38.03 1.85
2258 3342 5.639757 TGTTCATCATGCGTTGAATAAAGG 58.360 37.500 8.25 0.00 38.03 3.11
2259 3343 5.182950 TGTTCATCATGCGTTGAATAAAGGT 59.817 36.000 8.25 0.00 38.03 3.50
2260 3344 5.895636 TCATCATGCGTTGAATAAAGGTT 57.104 34.783 0.00 0.00 38.03 3.50
2261 3345 5.879237 TCATCATGCGTTGAATAAAGGTTC 58.121 37.500 0.00 0.00 38.03 3.62
2262 3346 4.695217 TCATGCGTTGAATAAAGGTTCC 57.305 40.909 0.00 0.00 0.00 3.62
2263 3347 4.331968 TCATGCGTTGAATAAAGGTTCCT 58.668 39.130 0.00 0.00 0.00 3.36
2264 3348 4.155826 TCATGCGTTGAATAAAGGTTCCTG 59.844 41.667 0.00 0.00 0.00 3.86
2265 3349 3.482436 TGCGTTGAATAAAGGTTCCTGT 58.518 40.909 0.00 0.00 0.00 4.00
2266 3350 4.643463 TGCGTTGAATAAAGGTTCCTGTA 58.357 39.130 0.00 0.00 0.00 2.74
2267 3351 5.064558 TGCGTTGAATAAAGGTTCCTGTAA 58.935 37.500 0.00 0.00 0.00 2.41
2268 3352 5.049267 TGCGTTGAATAAAGGTTCCTGTAAC 60.049 40.000 0.00 0.00 37.36 2.50
2269 3353 5.180680 GCGTTGAATAAAGGTTCCTGTAACT 59.819 40.000 0.00 0.00 38.23 2.24
2270 3354 6.293790 GCGTTGAATAAAGGTTCCTGTAACTT 60.294 38.462 0.00 0.00 38.23 2.66
2271 3355 7.645402 CGTTGAATAAAGGTTCCTGTAACTTT 58.355 34.615 0.00 0.00 38.91 2.66
2272 3356 8.776470 CGTTGAATAAAGGTTCCTGTAACTTTA 58.224 33.333 0.00 0.00 36.45 1.85
2343 3427 9.179552 TGTTCACATATTTCAAGAAAATGTTCG 57.820 29.630 14.72 9.16 38.08 3.95
2344 3428 9.180678 GTTCACATATTTCAAGAAAATGTTCGT 57.819 29.630 14.72 0.00 38.08 3.85
2345 3429 8.726650 TCACATATTTCAAGAAAATGTTCGTG 57.273 30.769 5.28 5.28 42.56 4.35
2346 3430 8.563732 TCACATATTTCAAGAAAATGTTCGTGA 58.436 29.630 9.87 9.87 46.36 4.35
2355 3439 9.958234 TCAAGAAAATGTTCGTGAATATTTTGA 57.042 25.926 25.04 17.64 45.47 2.69
2467 3551 6.819397 AAGGCATACTAAAGAAAGTTCACC 57.181 37.500 0.00 0.00 0.00 4.02
2468 3552 6.128138 AGGCATACTAAAGAAAGTTCACCT 57.872 37.500 0.00 0.00 0.00 4.00
2469 3553 7.253905 AGGCATACTAAAGAAAGTTCACCTA 57.746 36.000 0.00 0.00 0.00 3.08
2470 3554 7.686434 AGGCATACTAAAGAAAGTTCACCTAA 58.314 34.615 0.00 0.00 0.00 2.69
2471 3555 8.329502 AGGCATACTAAAGAAAGTTCACCTAAT 58.670 33.333 0.00 0.00 0.00 1.73
2472 3556 9.609346 GGCATACTAAAGAAAGTTCACCTAATA 57.391 33.333 0.00 0.00 0.00 0.98
2523 3607 9.927668 CATTTAATAAAATGTATGTGATCCCCC 57.072 33.333 3.26 0.00 44.62 5.40
2524 3608 7.753309 TTAATAAAATGTATGTGATCCCCCG 57.247 36.000 0.00 0.00 0.00 5.73
2525 3609 3.662759 AAAATGTATGTGATCCCCCGT 57.337 42.857 0.00 0.00 0.00 5.28
2526 3610 4.781775 AAAATGTATGTGATCCCCCGTA 57.218 40.909 0.00 0.00 0.00 4.02
2527 3611 4.781775 AAATGTATGTGATCCCCCGTAA 57.218 40.909 0.00 0.00 0.00 3.18
2528 3612 4.781775 AATGTATGTGATCCCCCGTAAA 57.218 40.909 0.00 0.00 0.00 2.01
2529 3613 4.781775 ATGTATGTGATCCCCCGTAAAA 57.218 40.909 0.00 0.00 0.00 1.52
2530 3614 4.571369 TGTATGTGATCCCCCGTAAAAA 57.429 40.909 0.00 0.00 0.00 1.94
2557 3641 9.965748 AAATGTGACATTTAAAAACGTTTTGAG 57.034 25.926 25.83 15.71 28.18 3.02
2558 3642 6.983910 TGTGACATTTAAAAACGTTTTGAGC 58.016 32.000 25.83 12.01 0.00 4.26
2559 3643 6.586463 TGTGACATTTAAAAACGTTTTGAGCA 59.414 30.769 25.83 14.06 0.00 4.26
2560 3644 7.276658 TGTGACATTTAAAAACGTTTTGAGCAT 59.723 29.630 25.83 12.88 0.00 3.79
2561 3645 8.113675 GTGACATTTAAAAACGTTTTGAGCATT 58.886 29.630 25.83 12.19 0.00 3.56
2562 3646 8.660373 TGACATTTAAAAACGTTTTGAGCATTT 58.340 25.926 25.83 11.49 0.00 2.32
2563 3647 9.142993 GACATTTAAAAACGTTTTGAGCATTTC 57.857 29.630 25.83 12.92 0.00 2.17
2564 3648 8.660373 ACATTTAAAAACGTTTTGAGCATTTCA 58.340 25.926 25.83 0.00 0.00 2.69
2565 3649 9.483062 CATTTAAAAACGTTTTGAGCATTTCAA 57.517 25.926 25.83 9.01 43.92 2.69
2580 3664 9.571810 TGAGCATTTCAAATATATGTTTGTGAC 57.428 29.630 20.33 11.73 39.50 3.67
2581 3665 9.571810 GAGCATTTCAAATATATGTTTGTGACA 57.428 29.630 20.33 3.14 43.71 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 988 1.473258 AACGTGCATTGCCCATACAT 58.527 45.000 6.12 0.00 0.00 2.29
17 993 1.539157 TATCAAACGTGCATTGCCCA 58.461 45.000 6.12 0.00 0.00 5.36
19 995 4.148696 GCATAATATCAAACGTGCATTGCC 59.851 41.667 6.12 0.00 33.09 4.52
40 1016 3.078097 ACGTGTGCAATTAATACCTGCA 58.922 40.909 8.83 8.83 43.54 4.41
96 1072 2.346766 TTGCCATCACCGCTAATCAT 57.653 45.000 0.00 0.00 0.00 2.45
148 1124 4.284123 GGTGAGCGCTCAACATGA 57.716 55.556 42.62 19.11 46.18 3.07
182 1158 3.650942 ACTCAGGTCAATCCAACAACCTA 59.349 43.478 0.00 0.00 40.13 3.08
183 1159 2.443255 ACTCAGGTCAATCCAACAACCT 59.557 45.455 0.00 0.00 42.87 3.50
184 1160 2.863809 ACTCAGGTCAATCCAACAACC 58.136 47.619 0.00 0.00 39.02 3.77
185 1161 3.882888 TCAACTCAGGTCAATCCAACAAC 59.117 43.478 0.00 0.00 39.02 3.32
277 1254 9.640963 GTTTGTTCTTCTAAATAGAGCTCTACA 57.359 33.333 25.52 14.34 33.21 2.74
453 1431 4.439700 GGATCATGCCAAATCTTGTGTCAG 60.440 45.833 0.00 0.00 0.00 3.51
454 1432 3.444742 GGATCATGCCAAATCTTGTGTCA 59.555 43.478 0.00 0.00 0.00 3.58
455 1433 3.698040 AGGATCATGCCAAATCTTGTGTC 59.302 43.478 0.00 0.00 0.00 3.67
479 1457 1.004918 CTGACGTCCTTTCGCCCTT 60.005 57.895 14.12 0.00 0.00 3.95
498 1477 2.029380 AGTAGTGTGCACATCGTTGCTA 60.029 45.455 24.69 15.13 43.41 3.49
592 1571 9.175060 GCTCTTAAGAAAATGACTCAGTTTTTC 57.825 33.333 6.63 6.60 38.84 2.29
595 1574 6.706270 TCGCTCTTAAGAAAATGACTCAGTTT 59.294 34.615 6.63 4.16 34.34 2.66
728 1707 2.703007 AGGGTACTTGCTGAGATCATCC 59.297 50.000 0.00 0.00 0.00 3.51
732 1711 3.357166 CGTAGGGTACTTGCTGAGATC 57.643 52.381 0.00 0.00 0.00 2.75
780 1759 4.783667 CGAACAACGGGAAGGGAA 57.216 55.556 0.00 0.00 38.46 3.97
809 1788 2.292016 TGGTGTTGATGAAATTTCGCGT 59.708 40.909 13.34 2.26 0.00 6.01
822 1801 3.629855 TCTCGCTTGATTTTTGGTGTTGA 59.370 39.130 0.00 0.00 0.00 3.18
825 1804 3.003689 CAGTCTCGCTTGATTTTTGGTGT 59.996 43.478 0.00 0.00 0.00 4.16
828 1807 2.589014 GCAGTCTCGCTTGATTTTTGG 58.411 47.619 0.00 0.00 0.00 3.28
829 1808 2.589014 GGCAGTCTCGCTTGATTTTTG 58.411 47.619 0.00 0.00 0.00 2.44
838 1817 2.359230 GCTTTGGGCAGTCTCGCT 60.359 61.111 0.00 0.00 41.35 4.93
864 1843 3.119096 GCGTCCTGGCCGTTCTTC 61.119 66.667 0.00 0.00 0.00 2.87
894 1873 7.272731 CGATCGTGTTCGTGATGGTATTTATAT 59.727 37.037 7.03 0.00 38.33 0.86
932 1911 0.386731 GCGTTGGTGAAATGGGTTCG 60.387 55.000 0.00 0.00 39.30 3.95
933 1912 0.671251 TGCGTTGGTGAAATGGGTTC 59.329 50.000 0.00 0.00 36.70 3.62
934 1913 1.272212 GATGCGTTGGTGAAATGGGTT 59.728 47.619 0.00 0.00 0.00 4.11
950 1933 3.554692 CGTGAAGGCGACGGATGC 61.555 66.667 0.00 0.00 33.08 3.91
969 1952 2.232452 CTGAACTGGACTAGTGACCTGG 59.768 54.545 0.00 0.00 40.26 4.45
978 1961 0.246635 GCGCTTCCTGAACTGGACTA 59.753 55.000 0.00 0.00 35.58 2.59
982 1965 0.392193 ATCTGCGCTTCCTGAACTGG 60.392 55.000 9.73 0.00 0.00 4.00
993 1976 2.444706 TAGGAGGCCATCTGCGCT 60.445 61.111 9.73 0.00 42.61 5.92
1176 2162 3.333189 CCCAGCGCGATGATGACG 61.333 66.667 28.29 8.39 35.47 4.35
1260 2246 2.437180 TCGAAGCGGGAGAGCGTA 60.437 61.111 0.00 0.00 43.00 4.42
1308 2294 2.249139 GTGAGGTTGTACTGGAGGACT 58.751 52.381 0.00 0.00 0.00 3.85
1398 2384 4.409218 AAGCGCTCGCCGTCGTAA 62.409 61.111 12.06 0.00 43.17 3.18
1903 2892 7.094975 ACGAATTCAAGGTGTCGAATTATTCAA 60.095 33.333 6.22 0.00 40.90 2.69
1930 2919 6.996562 TCGCAATATAATACGGTGTAACAG 57.003 37.500 0.00 0.00 39.98 3.16
1968 2957 8.664798 CGAGACCATGTCAAAATATGAACTAAA 58.335 33.333 0.00 0.00 40.50 1.85
1969 2958 7.822334 ACGAGACCATGTCAAAATATGAACTAA 59.178 33.333 0.00 0.00 40.50 2.24
1970 2959 7.277760 CACGAGACCATGTCAAAATATGAACTA 59.722 37.037 0.00 0.00 40.50 2.24
1971 2960 6.092670 CACGAGACCATGTCAAAATATGAACT 59.907 38.462 0.00 0.00 40.50 3.01
1987 2976 2.552599 TTTATGTTGCCACGAGACCA 57.447 45.000 0.00 0.00 0.00 4.02
2013 3002 7.706281 ACATATTTGAAATGTTTTTGCGTGA 57.294 28.000 0.00 0.00 33.83 4.35
2014 3003 8.060679 TCAACATATTTGAAATGTTTTTGCGTG 58.939 29.630 0.00 0.00 43.31 5.34
2015 3004 8.136057 TCAACATATTTGAAATGTTTTTGCGT 57.864 26.923 0.00 0.00 43.31 5.24
2016 3005 9.042632 CATCAACATATTTGAAATGTTTTTGCG 57.957 29.630 0.00 0.00 43.31 4.85
2018 3007 9.880064 TGCATCAACATATTTGAAATGTTTTTG 57.120 25.926 0.00 0.84 43.31 2.44
2021 3104 7.148373 GGCTGCATCAACATATTTGAAATGTTT 60.148 33.333 0.50 0.00 43.31 2.83
2037 3120 5.105797 CCACTAGTTATTTTGGCTGCATCAA 60.106 40.000 0.50 0.00 0.00 2.57
2039 3122 4.640201 TCCACTAGTTATTTTGGCTGCATC 59.360 41.667 0.50 0.00 0.00 3.91
2061 3145 1.047801 AAGGGTGGGTTTGTTGCATC 58.952 50.000 0.00 0.00 0.00 3.91
2062 3146 0.758123 CAAGGGTGGGTTTGTTGCAT 59.242 50.000 0.00 0.00 0.00 3.96
2067 3151 2.123033 GGCCAAGGGTGGGTTTGT 60.123 61.111 0.00 0.00 46.09 2.83
2068 3152 0.252012 TATGGCCAAGGGTGGGTTTG 60.252 55.000 10.96 0.00 46.09 2.93
2072 3156 2.123726 GCTATGGCCAAGGGTGGG 60.124 66.667 10.96 0.00 46.09 4.61
2075 3159 0.475906 GATCTGCTATGGCCAAGGGT 59.524 55.000 10.96 0.00 37.74 4.34
2078 3162 1.224075 CGTGATCTGCTATGGCCAAG 58.776 55.000 10.96 10.17 37.74 3.61
2091 3175 5.970612 TGCATATGTTATGTTTTGCGTGATC 59.029 36.000 4.29 0.00 32.90 2.92
2097 3181 5.806502 TCTTGCTGCATATGTTATGTTTTGC 59.193 36.000 1.84 0.00 0.00 3.68
2100 3184 6.038356 GCTTCTTGCTGCATATGTTATGTTT 58.962 36.000 1.84 0.00 38.95 2.83
2125 3209 4.127566 AGTTGCAAGTGTTCTTTGCAAT 57.872 36.364 23.01 12.56 42.78 3.56
2174 3258 9.793252 CGAGGTGATATTTTTCATTTCAGAAAT 57.207 29.630 2.20 2.20 37.35 2.17
2175 3259 7.754924 GCGAGGTGATATTTTTCATTTCAGAAA 59.245 33.333 0.00 0.00 35.82 2.52
2176 3260 7.094420 TGCGAGGTGATATTTTTCATTTCAGAA 60.094 33.333 0.00 0.00 0.00 3.02
2177 3261 6.374053 TGCGAGGTGATATTTTTCATTTCAGA 59.626 34.615 0.00 0.00 0.00 3.27
2178 3262 6.554419 TGCGAGGTGATATTTTTCATTTCAG 58.446 36.000 0.00 0.00 0.00 3.02
2179 3263 6.507958 TGCGAGGTGATATTTTTCATTTCA 57.492 33.333 0.00 0.00 0.00 2.69
2180 3264 7.810766 TTTGCGAGGTGATATTTTTCATTTC 57.189 32.000 0.00 0.00 0.00 2.17
2181 3265 8.600449 TTTTTGCGAGGTGATATTTTTCATTT 57.400 26.923 0.00 0.00 0.00 2.32
2224 3308 9.596677 CAACGCATGATGAACATTTTTAAAATT 57.403 25.926 0.55 0.00 37.07 1.82
2225 3309 8.986847 TCAACGCATGATGAACATTTTTAAAAT 58.013 25.926 0.55 0.00 37.07 1.82
2226 3310 8.357796 TCAACGCATGATGAACATTTTTAAAA 57.642 26.923 0.00 0.00 37.07 1.52
2227 3311 7.936950 TCAACGCATGATGAACATTTTTAAA 57.063 28.000 0.00 0.00 37.07 1.52
2228 3312 7.936950 TTCAACGCATGATGAACATTTTTAA 57.063 28.000 0.00 0.00 38.03 1.52
2229 3313 9.631452 TTATTCAACGCATGATGAACATTTTTA 57.369 25.926 10.10 0.00 39.34 1.52
2230 3314 8.531622 TTATTCAACGCATGATGAACATTTTT 57.468 26.923 10.10 0.00 39.34 1.94
2231 3315 8.531622 TTTATTCAACGCATGATGAACATTTT 57.468 26.923 10.10 0.21 39.34 1.82
2232 3316 7.276218 CCTTTATTCAACGCATGATGAACATTT 59.724 33.333 10.10 0.49 39.34 2.32
2233 3317 6.753279 CCTTTATTCAACGCATGATGAACATT 59.247 34.615 10.10 0.76 39.34 2.71
2234 3318 6.127647 ACCTTTATTCAACGCATGATGAACAT 60.128 34.615 10.10 0.00 39.34 2.71
2235 3319 5.182950 ACCTTTATTCAACGCATGATGAACA 59.817 36.000 10.10 0.00 39.34 3.18
2236 3320 5.640732 ACCTTTATTCAACGCATGATGAAC 58.359 37.500 10.10 0.00 39.34 3.18
2237 3321 5.895636 ACCTTTATTCAACGCATGATGAA 57.104 34.783 0.00 4.13 40.57 2.57
2238 3322 5.163663 GGAACCTTTATTCAACGCATGATGA 60.164 40.000 0.00 0.00 38.03 2.92
2239 3323 5.036737 GGAACCTTTATTCAACGCATGATG 58.963 41.667 0.00 0.00 38.03 3.07
2240 3324 4.949856 AGGAACCTTTATTCAACGCATGAT 59.050 37.500 0.00 0.00 38.03 2.45
2241 3325 4.155826 CAGGAACCTTTATTCAACGCATGA 59.844 41.667 0.00 0.00 35.85 3.07
2242 3326 4.082787 ACAGGAACCTTTATTCAACGCATG 60.083 41.667 0.00 0.00 0.00 4.06
2243 3327 4.079253 ACAGGAACCTTTATTCAACGCAT 58.921 39.130 0.00 0.00 0.00 4.73
2244 3328 3.482436 ACAGGAACCTTTATTCAACGCA 58.518 40.909 0.00 0.00 0.00 5.24
2245 3329 5.180680 AGTTACAGGAACCTTTATTCAACGC 59.819 40.000 0.00 0.00 39.02 4.84
2246 3330 6.796705 AGTTACAGGAACCTTTATTCAACG 57.203 37.500 0.00 0.00 39.02 4.10
2317 3401 9.179552 CGAACATTTTCTTGAAATATGTGAACA 57.820 29.630 16.54 0.00 35.79 3.18
2318 3402 9.180678 ACGAACATTTTCTTGAAATATGTGAAC 57.819 29.630 16.54 12.67 35.79 3.18
2319 3403 9.179552 CACGAACATTTTCTTGAAATATGTGAA 57.820 29.630 16.54 0.00 35.79 3.18
2320 3404 8.563732 TCACGAACATTTTCTTGAAATATGTGA 58.436 29.630 16.54 12.58 37.14 3.58
2321 3405 8.726650 TCACGAACATTTTCTTGAAATATGTG 57.273 30.769 16.54 11.26 37.14 3.21
2322 3406 9.912634 ATTCACGAACATTTTCTTGAAATATGT 57.087 25.926 15.02 13.09 46.94 2.29
2329 3413 9.958234 TCAAAATATTCACGAACATTTTCTTGA 57.042 25.926 5.92 0.00 38.03 3.02
2441 3525 8.141909 GGTGAACTTTCTTTAGTATGCCTTTTT 58.858 33.333 0.00 0.00 0.00 1.94
2442 3526 7.505923 AGGTGAACTTTCTTTAGTATGCCTTTT 59.494 33.333 0.00 0.00 0.00 2.27
2443 3527 7.004691 AGGTGAACTTTCTTTAGTATGCCTTT 58.995 34.615 0.00 0.00 0.00 3.11
2444 3528 6.543735 AGGTGAACTTTCTTTAGTATGCCTT 58.456 36.000 0.00 0.00 0.00 4.35
2445 3529 6.128138 AGGTGAACTTTCTTTAGTATGCCT 57.872 37.500 0.00 0.00 0.00 4.75
2446 3530 7.916914 TTAGGTGAACTTTCTTTAGTATGCC 57.083 36.000 0.00 0.00 0.00 4.40
2498 3582 8.802267 CGGGGGATCACATACATTTTATTAAAT 58.198 33.333 0.00 0.00 34.29 1.40
2499 3583 7.780745 ACGGGGGATCACATACATTTTATTAAA 59.219 33.333 0.00 0.00 0.00 1.52
2500 3584 7.291566 ACGGGGGATCACATACATTTTATTAA 58.708 34.615 0.00 0.00 0.00 1.40
2501 3585 6.843752 ACGGGGGATCACATACATTTTATTA 58.156 36.000 0.00 0.00 0.00 0.98
2502 3586 5.701224 ACGGGGGATCACATACATTTTATT 58.299 37.500 0.00 0.00 0.00 1.40
2503 3587 5.319043 ACGGGGGATCACATACATTTTAT 57.681 39.130 0.00 0.00 0.00 1.40
2504 3588 4.781775 ACGGGGGATCACATACATTTTA 57.218 40.909 0.00 0.00 0.00 1.52
2505 3589 3.662759 ACGGGGGATCACATACATTTT 57.337 42.857 0.00 0.00 0.00 1.82
2506 3590 4.781775 TTACGGGGGATCACATACATTT 57.218 40.909 0.00 0.00 0.00 2.32
2507 3591 4.781775 TTTACGGGGGATCACATACATT 57.218 40.909 0.00 0.00 0.00 2.71
2508 3592 4.781775 TTTTACGGGGGATCACATACAT 57.218 40.909 0.00 0.00 0.00 2.29
2509 3593 4.571369 TTTTTACGGGGGATCACATACA 57.429 40.909 0.00 0.00 0.00 2.29
2531 3615 9.965748 CTCAAAACGTTTTTAAATGTCACATTT 57.034 25.926 23.14 19.55 37.16 2.32
2532 3616 8.113675 GCTCAAAACGTTTTTAAATGTCACATT 58.886 29.630 23.14 0.00 37.16 2.71
2533 3617 7.276658 TGCTCAAAACGTTTTTAAATGTCACAT 59.723 29.630 23.14 0.00 37.16 3.21
2534 3618 6.586463 TGCTCAAAACGTTTTTAAATGTCACA 59.414 30.769 23.14 9.80 37.16 3.58
2535 3619 6.983910 TGCTCAAAACGTTTTTAAATGTCAC 58.016 32.000 23.14 7.66 37.16 3.67
2536 3620 7.763172 ATGCTCAAAACGTTTTTAAATGTCA 57.237 28.000 23.14 14.13 37.16 3.58
2537 3621 9.142993 GAAATGCTCAAAACGTTTTTAAATGTC 57.857 29.630 23.14 14.30 37.16 3.06
2538 3622 8.660373 TGAAATGCTCAAAACGTTTTTAAATGT 58.340 25.926 23.14 10.04 39.69 2.71
2539 3623 9.483062 TTGAAATGCTCAAAACGTTTTTAAATG 57.517 25.926 23.14 12.89 41.21 2.32
2554 3638 9.571810 GTCACAAACATATATTTGAAATGCTCA 57.428 29.630 13.29 0.00 41.28 4.26
2555 3639 9.571810 TGTCACAAACATATATTTGAAATGCTC 57.428 29.630 13.29 0.45 41.28 4.26


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

AutoCloner maintained by Alex Coulton.