Multiple sequence alignment - TraesCS1D01G306200

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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 TraesCS1D01G306200 chr1D 100.000 2792 0 0 1 2792 403337143 403334352 0.000000e+00 5156.0
1 TraesCS1D01G306200 chr1D 88.499 713 81 1 1079 1790 472561007 472561719 0.000000e+00 861.0
2 TraesCS1D01G306200 chr1D 100.000 40 0 0 2203 2242 403334902 403334863 1.070000e-09 75.0
3 TraesCS1D01G306200 chr1D 100.000 40 0 0 2242 2281 403334941 403334902 1.070000e-09 75.0
4 TraesCS1D01G306200 chr1B 91.574 2065 106 37 1 2012 542580991 542578942 0.000000e+00 2787.0
5 TraesCS1D01G306200 chr1B 91.171 1563 97 10 638 2189 542432867 542431335 0.000000e+00 2084.0
6 TraesCS1D01G306200 chr1B 88.079 713 84 1 1079 1790 657272156 657272868 0.000000e+00 845.0
7 TraesCS1D01G306200 chr1B 87.925 530 33 8 2265 2792 542430695 542430195 1.850000e-166 595.0
8 TraesCS1D01G306200 chr1A 91.745 1805 95 28 450 2219 498598133 498596348 0.000000e+00 2459.0
9 TraesCS1D01G306200 chr1A 88.079 713 84 1 1079 1790 566564264 566564976 0.000000e+00 845.0
10 TraesCS1D01G306200 chr1A 87.194 531 47 9 2265 2792 498595734 498595222 4.010000e-163 584.0
11 TraesCS1D01G306200 chr1A 95.455 242 11 0 173 414 498598373 498598132 1.210000e-103 387.0
12 TraesCS1D01G306200 chr1A 90.833 120 9 2 3 121 498598503 498598385 2.880000e-35 159.0
13 TraesCS1D01G306200 chr5B 88.382 723 84 0 1070 1792 532876737 532877459 0.000000e+00 870.0
14 TraesCS1D01G306200 chr5A 87.967 723 87 0 1070 1792 553420966 553421688 0.000000e+00 854.0
15 TraesCS1D01G306200 chr5D 87.828 723 88 0 1070 1792 438360055 438360777 0.000000e+00 848.0
16 TraesCS1D01G306200 chr6B 92.262 168 8 2 316 479 117318313 117318147 1.670000e-57 233.0
17 TraesCS1D01G306200 chr6B 92.593 135 10 0 1 135 117323791 117323657 7.890000e-46 195.0
18 TraesCS1D01G306200 chr6B 89.888 89 3 4 153 236 117317080 117316993 2.940000e-20 110.0
19 TraesCS1D01G306200 chr3B 100.000 29 0 0 474 502 571535864 571535892 1.000000e-03 54.7
20 TraesCS1D01G306200 chr3B 100.000 28 0 0 478 505 607715106 607715133 5.000000e-03 52.8
21 TraesCS1D01G306200 chr4B 100.000 28 0 0 475 502 2210939 2210912 5.000000e-03 52.8
22 TraesCS1D01G306200 chr4B 100.000 28 0 0 475 502 2240929 2240902 5.000000e-03 52.8
23 TraesCS1D01G306200 chr3D 100.000 28 0 0 475 502 462453853 462453880 5.000000e-03 52.8
24 TraesCS1D01G306200 chr3A 100.000 28 0 0 475 502 605239721 605239748 5.000000e-03 52.8
25 TraesCS1D01G306200 chr2B 100.000 28 0 0 476 503 724550982 724551009 5.000000e-03 52.8


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 TraesCS1D01G306200 chr1D 403334352 403337143 2791 True 1768.666667 5156 100.00000 1 2792 3 chr1D.!!$R1 2791
1 TraesCS1D01G306200 chr1D 472561007 472561719 712 False 861.000000 861 88.49900 1079 1790 1 chr1D.!!$F1 711
2 TraesCS1D01G306200 chr1B 542578942 542580991 2049 True 2787.000000 2787 91.57400 1 2012 1 chr1B.!!$R1 2011
3 TraesCS1D01G306200 chr1B 542430195 542432867 2672 True 1339.500000 2084 89.54800 638 2792 2 chr1B.!!$R2 2154
4 TraesCS1D01G306200 chr1B 657272156 657272868 712 False 845.000000 845 88.07900 1079 1790 1 chr1B.!!$F1 711
5 TraesCS1D01G306200 chr1A 498595222 498598503 3281 True 897.250000 2459 91.30675 3 2792 4 chr1A.!!$R1 2789
6 TraesCS1D01G306200 chr1A 566564264 566564976 712 False 845.000000 845 88.07900 1079 1790 1 chr1A.!!$F1 711
7 TraesCS1D01G306200 chr5B 532876737 532877459 722 False 870.000000 870 88.38200 1070 1792 1 chr5B.!!$F1 722
8 TraesCS1D01G306200 chr5A 553420966 553421688 722 False 854.000000 854 87.96700 1070 1792 1 chr5A.!!$F1 722
9 TraesCS1D01G306200 chr5D 438360055 438360777 722 False 848.000000 848 87.82800 1070 1792 1 chr5D.!!$F1 722

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
867 878 0.622665 GATAGGCCCATCCATCCAGG 59.377 60.0 0.0 0.0 37.29 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 3245 0.371301 CAACGATGCTGATGGTCACG 59.629 55.0 0.0 0.0 0.0 4.35 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
149 151 7.671302 ACACTTATATCTGTAAGGTGGCATAG 58.329 38.462 0.00 0.00 36.27 2.23
168 170 5.009110 GCATAGAAAGGGTAAATTCCTCTGC 59.991 44.000 0.00 0.00 32.59 4.26
195 197 8.031277 ACTTTTGATGAATATTTTGCTGACCTC 58.969 33.333 0.00 0.00 0.00 3.85
236 238 5.071250 TGAAAGTTGGGAAGAAGTGCTACTA 59.929 40.000 0.00 0.00 0.00 1.82
244 246 6.214819 TGGGAAGAAGTGCTACTAGGTTTATT 59.785 38.462 0.00 0.00 0.00 1.40
351 353 1.246056 TGCAGAAGCTGAATGTGGCC 61.246 55.000 0.00 0.00 42.74 5.36
493 496 7.887996 ACGTCCGTCTTATATTTGTTTACAA 57.112 32.000 0.00 0.00 0.00 2.41
630 638 7.038729 TGCCTTTAATTGTTACCATGGATCAAA 60.039 33.333 21.47 7.93 0.00 2.69
632 640 9.889128 CCTTTAATTGTTACCATGGATCAAATT 57.111 29.630 21.47 18.96 0.00 1.82
634 642 9.664332 TTTAATTGTTACCATGGATCAAATTGG 57.336 29.630 21.47 0.00 35.31 3.16
635 643 4.734398 TGTTACCATGGATCAAATTGGC 57.266 40.909 21.47 0.00 32.26 4.52
636 644 4.352009 TGTTACCATGGATCAAATTGGCT 58.648 39.130 21.47 0.00 32.26 4.75
818 829 4.201792 GCATGCTAAGACACAATCACAGAG 60.202 45.833 11.37 0.00 0.00 3.35
867 878 0.622665 GATAGGCCCATCCATCCAGG 59.377 60.000 0.00 0.00 37.29 4.45
878 889 1.651240 CCATCCAGGCAAAGCGTCAG 61.651 60.000 0.00 0.00 0.00 3.51
903 921 1.298014 CAAGGCCCCTCACAGTCTC 59.702 63.158 0.00 0.00 0.00 3.36
986 1006 3.636300 AGCACAAGACAAGCAACCAAATA 59.364 39.130 0.00 0.00 0.00 1.40
1005 1037 2.822707 ATTCTTCCTCTGCAATGGCT 57.177 45.000 0.00 0.00 41.91 4.75
1006 1038 1.830279 TTCTTCCTCTGCAATGGCTG 58.170 50.000 0.00 0.00 41.91 4.85
1041 1073 4.332543 TCCTCCCCGGGTCTTGCT 62.333 66.667 21.85 0.00 0.00 3.91
1054 1092 2.033911 TTGCTGCGGCCAAGATCA 59.966 55.556 16.57 0.00 37.74 2.92
1055 1093 1.378911 TTGCTGCGGCCAAGATCAT 60.379 52.632 16.57 0.00 37.74 2.45
1215 1253 3.382832 CTCACCGGCGAGTTCCCT 61.383 66.667 9.30 0.00 0.00 4.20
1224 1262 2.017559 GCGAGTTCCCTGGCGACTAT 62.018 60.000 0.00 0.00 32.57 2.12
1338 1376 2.032528 CTTGGCTGCGTCTTCCCA 59.967 61.111 0.00 0.00 0.00 4.37
1344 1382 1.294780 CTGCGTCTTCCCAGAGCTT 59.705 57.895 0.00 0.00 0.00 3.74
1347 1385 0.036858 GCGTCTTCCCAGAGCTTCTT 60.037 55.000 0.00 0.00 0.00 2.52
1401 1439 2.687935 GTGGTTCAAAGCTGGTTCTCAA 59.312 45.455 0.00 0.00 0.00 3.02
1455 1493 2.036098 CCCAGCCTTGTCCATGCA 59.964 61.111 0.00 0.00 0.00 3.96
1680 1718 2.554032 CTCCATGTTTGGCTTCTTCGTT 59.446 45.455 0.00 0.00 43.29 3.85
1743 1781 4.873129 CACCTCGCCGATCCCGTG 62.873 72.222 0.00 0.00 0.00 4.94
1815 1853 2.044946 GGCGATGCCTGTTCCCTT 60.045 61.111 0.00 0.00 46.69 3.95
1879 1935 2.436646 CAAGGGCTACTGCGGGTG 60.437 66.667 0.00 0.00 40.82 4.61
1930 1986 5.463392 CCGATGAGGACATGTAACAGTATTG 59.537 44.000 0.00 0.00 45.00 1.90
2030 2092 8.230472 ACTGAAATTCTCTCTGAAACAAATGT 57.770 30.769 0.00 0.00 38.29 2.71
2039 2101 5.932303 TCTCTGAAACAAATGTACAGTAGGC 59.068 40.000 0.33 0.00 35.58 3.93
2086 2148 6.039382 GCCAAGGACTACAAAAGAAGAAGAAA 59.961 38.462 0.00 0.00 0.00 2.52
2149 2219 5.223449 AGTAGCTGTACAACTTTAAGGCA 57.777 39.130 3.72 0.00 0.00 4.75
2175 2245 2.076100 TGCGCTCATGGTTTAAGTCAG 58.924 47.619 9.73 0.00 0.00 3.51
2191 2261 3.454371 GTCAGTACAAGTGACAGGTGT 57.546 47.619 9.47 0.00 45.49 4.16
2201 2271 0.178955 TGACAGGTGTTCCCTCCGTA 60.179 55.000 0.00 0.00 43.86 4.02
2202 2272 0.245813 GACAGGTGTTCCCTCCGTAC 59.754 60.000 0.00 0.00 43.86 3.67
2216 2286 4.323257 CCCTCCGTACCAAAATGTAAGACT 60.323 45.833 0.00 0.00 0.00 3.24
2219 2289 6.479001 CCTCCGTACCAAAATGTAAGACTATG 59.521 42.308 0.00 0.00 0.00 2.23
2220 2290 5.813672 TCCGTACCAAAATGTAAGACTATGC 59.186 40.000 0.00 0.00 0.00 3.14
2221 2291 5.583061 CCGTACCAAAATGTAAGACTATGCA 59.417 40.000 0.00 0.00 0.00 3.96
2222 2292 6.092944 CCGTACCAAAATGTAAGACTATGCAA 59.907 38.462 0.00 0.00 0.00 4.08
2223 2293 7.201696 CCGTACCAAAATGTAAGACTATGCAAT 60.202 37.037 0.00 0.00 0.00 3.56
2236 2306 7.206981 AGACTATGCAATATACACATTTGCC 57.793 36.000 5.73 0.00 43.91 4.52
2237 2307 6.772233 AGACTATGCAATATACACATTTGCCA 59.228 34.615 5.73 0.00 43.91 4.92
2238 2308 7.449395 AGACTATGCAATATACACATTTGCCAT 59.551 33.333 5.73 3.27 43.91 4.40
2239 2309 7.954835 ACTATGCAATATACACATTTGCCATT 58.045 30.769 5.73 0.00 43.91 3.16
2240 2310 8.084073 ACTATGCAATATACACATTTGCCATTC 58.916 33.333 5.73 0.00 43.91 2.67
2241 2311 5.599732 TGCAATATACACATTTGCCATTCC 58.400 37.500 5.73 0.00 43.91 3.01
2242 2312 4.990426 GCAATATACACATTTGCCATTCCC 59.010 41.667 0.00 0.00 39.80 3.97
2243 2313 5.453057 GCAATATACACATTTGCCATTCCCA 60.453 40.000 0.00 0.00 39.80 4.37
2244 2314 6.580788 CAATATACACATTTGCCATTCCCAA 58.419 36.000 0.00 0.00 0.00 4.12
2245 2315 6.805016 ATATACACATTTGCCATTCCCAAA 57.195 33.333 0.00 0.00 36.70 3.28
2246 2316 3.853355 ACACATTTGCCATTCCCAAAA 57.147 38.095 0.00 0.00 35.97 2.44
2248 2318 4.073549 ACACATTTGCCATTCCCAAAATG 58.926 39.130 5.64 5.64 35.97 2.32
2249 2319 4.073549 CACATTTGCCATTCCCAAAATGT 58.926 39.130 6.76 6.76 35.97 2.71
2250 2320 5.221803 ACACATTTGCCATTCCCAAAATGTA 60.222 36.000 11.12 0.00 35.55 2.29
2251 2321 5.704515 CACATTTGCCATTCCCAAAATGTAA 59.295 36.000 11.12 0.00 35.97 2.41
2252 2322 5.939296 ACATTTGCCATTCCCAAAATGTAAG 59.061 36.000 10.07 0.00 35.97 2.34
2253 2323 5.815233 TTTGCCATTCCCAAAATGTAAGA 57.185 34.783 0.00 0.00 29.93 2.10
2254 2324 4.799564 TGCCATTCCCAAAATGTAAGAC 57.200 40.909 0.00 0.00 0.00 3.01
2255 2325 4.415596 TGCCATTCCCAAAATGTAAGACT 58.584 39.130 0.00 0.00 0.00 3.24
2257 2327 6.194235 TGCCATTCCCAAAATGTAAGACTAT 58.806 36.000 0.00 0.00 0.00 2.12
2258 2328 6.096705 TGCCATTCCCAAAATGTAAGACTATG 59.903 38.462 0.00 0.00 0.00 2.23
2259 2329 6.507023 CCATTCCCAAAATGTAAGACTATGC 58.493 40.000 0.00 0.00 0.00 3.14
2260 2330 6.096705 CCATTCCCAAAATGTAAGACTATGCA 59.903 38.462 0.00 0.00 0.00 3.96
2263 2979 8.815565 TTCCCAAAATGTAAGACTATGCAATA 57.184 30.769 0.00 0.00 0.00 1.90
2278 2994 7.954835 ACTATGCAATATACACATTTGCCATT 58.045 30.769 5.73 0.00 43.91 3.16
2298 3014 3.865011 TCCGTGCGGTTACAATAAGTA 57.135 42.857 10.60 0.00 36.47 2.24
2299 3015 3.510719 TCCGTGCGGTTACAATAAGTAC 58.489 45.455 10.60 0.00 36.47 2.73
2302 3018 5.101628 CCGTGCGGTTACAATAAGTACTTA 58.898 41.667 17.41 17.41 30.91 2.24
2303 3019 5.004726 CCGTGCGGTTACAATAAGTACTTAC 59.995 44.000 17.45 6.45 30.91 2.34
2350 3067 6.609237 AATATCATCGCATGTACATATGGC 57.391 37.500 8.32 7.30 0.00 4.40
2391 3109 4.724074 TCATGGGCACTGATGAAATTTC 57.276 40.909 11.41 11.41 0.00 2.17
2408 3126 8.372877 TGAAATTTCAGGGGCTAAAAATCATA 57.627 30.769 16.91 0.00 32.50 2.15
2412 3130 7.823745 TTTCAGGGGCTAAAAATCATATCTC 57.176 36.000 0.00 0.00 0.00 2.75
2440 3158 2.927553 AATTTCATGCGAAGTCCTGC 57.072 45.000 0.00 0.00 31.28 4.85
2441 3159 1.098050 ATTTCATGCGAAGTCCTGCC 58.902 50.000 0.00 0.00 31.28 4.85
2442 3160 0.036732 TTTCATGCGAAGTCCTGCCT 59.963 50.000 0.00 0.00 31.28 4.75
2443 3161 0.391661 TTCATGCGAAGTCCTGCCTC 60.392 55.000 0.00 0.00 0.00 4.70
2444 3162 1.220206 CATGCGAAGTCCTGCCTCT 59.780 57.895 0.00 0.00 0.00 3.69
2445 3163 0.809241 CATGCGAAGTCCTGCCTCTC 60.809 60.000 0.00 0.00 0.00 3.20
2446 3164 1.260538 ATGCGAAGTCCTGCCTCTCA 61.261 55.000 0.00 0.00 0.00 3.27
2447 3165 1.153667 GCGAAGTCCTGCCTCTCAG 60.154 63.158 0.00 0.00 42.49 3.35
2448 3166 1.153667 CGAAGTCCTGCCTCTCAGC 60.154 63.158 0.00 0.00 41.50 4.26
2471 3189 4.130118 CTCTCAGGCAATTACCACCATAC 58.870 47.826 0.00 0.00 0.00 2.39
2472 3190 2.872245 CTCAGGCAATTACCACCATACG 59.128 50.000 0.00 0.00 0.00 3.06
2473 3191 1.333619 CAGGCAATTACCACCATACGC 59.666 52.381 0.00 0.00 0.00 4.42
2474 3192 0.666374 GGCAATTACCACCATACGCC 59.334 55.000 0.00 0.00 0.00 5.68
2475 3193 1.675552 GCAATTACCACCATACGCCT 58.324 50.000 0.00 0.00 0.00 5.52
2476 3194 2.485835 GGCAATTACCACCATACGCCTA 60.486 50.000 0.00 0.00 35.39 3.93
2480 3198 5.221165 GCAATTACCACCATACGCCTAATTT 60.221 40.000 0.00 0.00 0.00 1.82
2490 3208 6.829811 ACCATACGCCTAATTTAAAAGCCTTA 59.170 34.615 0.00 0.00 0.00 2.69
2491 3209 7.339976 ACCATACGCCTAATTTAAAAGCCTTAA 59.660 33.333 0.00 0.00 0.00 1.85
2524 3242 3.839046 ATACCCGCCCCGGCTATCA 62.839 63.158 3.84 0.00 46.86 2.15
2527 3245 4.910585 CCGCCCCGGCTATCACAC 62.911 72.222 3.84 0.00 41.17 3.82
2542 3260 0.723414 CACACGTGACCATCAGCATC 59.277 55.000 25.01 0.00 0.00 3.91
2553 3273 3.436704 ACCATCAGCATCGTTGTTTACAG 59.563 43.478 0.00 0.00 0.00 2.74
2581 3301 1.554160 AGAGTGATCTTGGAGGCTGTG 59.446 52.381 0.00 0.00 0.00 3.66
2584 3304 2.107204 AGTGATCTTGGAGGCTGTGTTT 59.893 45.455 0.00 0.00 0.00 2.83
2644 3364 1.338484 TGATCTCAGGCAGTTCAGCAC 60.338 52.381 0.00 0.00 35.83 4.40
2720 3440 6.052360 GGGAAATTGAAGGCAGTTTTTACAA 58.948 36.000 0.00 0.00 34.57 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
149 151 4.336280 AGTGCAGAGGAATTTACCCTTTC 58.664 43.478 0.00 0.00 33.36 2.62
168 170 7.816031 AGGTCAGCAAAATATTCATCAAAAGTG 59.184 33.333 0.00 0.00 0.00 3.16
266 268 5.620654 GCTGATGCATACACAACATCAAAGT 60.621 40.000 0.00 0.00 46.89 2.66
351 353 6.979817 TCAAATCCACTGAACACAAAAATCTG 59.020 34.615 0.00 0.00 0.00 2.90
493 496 6.779860 TGCTAATTTTCTGTTCTACTCCCTT 58.220 36.000 0.00 0.00 0.00 3.95
818 829 3.861840 TCCTCTGATTGGACAATTCGTC 58.138 45.455 0.00 0.90 44.57 4.20
867 878 2.253452 CTGGCACTGACGCTTTGC 59.747 61.111 0.00 0.00 35.40 3.68
903 921 7.649306 GCTGCATTGGAATTTAAATAGTACAGG 59.351 37.037 0.01 0.00 0.00 4.00
907 925 7.014230 GGGAGCTGCATTGGAATTTAAATAGTA 59.986 37.037 7.79 0.00 0.00 1.82
918 936 0.112995 AACAGGGAGCTGCATTGGAA 59.887 50.000 7.79 0.00 0.00 3.53
986 1006 2.376109 CAGCCATTGCAGAGGAAGAAT 58.624 47.619 10.40 0.00 41.13 2.40
1005 1037 3.899981 GAGTGCCATGGTGGACGCA 62.900 63.158 14.67 0.09 40.96 5.24
1006 1038 3.127533 GAGTGCCATGGTGGACGC 61.128 66.667 14.67 6.17 40.96 5.19
1041 1073 1.146930 GGAGATGATCTTGGCCGCA 59.853 57.895 0.00 0.00 0.00 5.69
1074 1112 1.750018 CATTGTGATGCGGCCCTCA 60.750 57.895 0.00 0.00 0.00 3.86
1215 1253 2.364973 TCCCAGCCATAGTCGCCA 60.365 61.111 0.00 0.00 0.00 5.69
1401 1439 1.604378 CCCACCCTCGCTGAAGATT 59.396 57.895 0.00 0.00 0.00 2.40
1455 1493 1.047596 AGATGGCGAGGATGCTCTGT 61.048 55.000 12.78 0.00 34.52 3.41
1743 1781 1.805428 ATGCCCAGGCGTTGTTGTTC 61.805 55.000 3.83 0.00 45.51 3.18
1815 1853 1.705002 CCATACATCCCAAGCCCCGA 61.705 60.000 0.00 0.00 0.00 5.14
1866 1922 2.337361 AAAAACACCCGCAGTAGCC 58.663 52.632 0.00 0.00 37.52 3.93
1930 1986 9.090692 CATCATTCTTGTTTGATAAACCAATCC 57.909 33.333 2.36 0.00 40.67 3.01
2030 2092 1.272313 ACCCTGAACTCGCCTACTGTA 60.272 52.381 0.00 0.00 0.00 2.74
2039 2101 1.151668 CTCTTGCAACCCTGAACTCG 58.848 55.000 0.00 0.00 0.00 4.18
2086 2148 5.227152 AGCACACTCGTTTGTTTTCTTTTT 58.773 33.333 0.00 0.00 0.00 1.94
2149 2219 1.032014 AAACCATGAGCGCACTTGTT 58.968 45.000 11.47 5.79 0.00 2.83
2157 2227 4.242475 TGTACTGACTTAAACCATGAGCG 58.758 43.478 0.00 0.00 0.00 5.03
2175 2245 2.490991 GGGAACACCTGTCACTTGTAC 58.509 52.381 0.00 0.00 35.85 2.90
2191 2261 4.286549 TCTTACATTTTGGTACGGAGGGAA 59.713 41.667 0.00 0.00 0.00 3.97
2219 2289 4.990426 GGGAATGGCAAATGTGTATATTGC 59.010 41.667 0.00 1.29 46.60 3.56
2220 2290 6.159299 TGGGAATGGCAAATGTGTATATTG 57.841 37.500 0.00 0.00 0.00 1.90
2221 2291 6.805016 TTGGGAATGGCAAATGTGTATATT 57.195 33.333 0.00 0.00 0.00 1.28
2222 2292 6.805016 TTTGGGAATGGCAAATGTGTATAT 57.195 33.333 0.00 0.00 0.00 0.86
2223 2293 6.611613 TTTTGGGAATGGCAAATGTGTATA 57.388 33.333 0.00 0.00 0.00 1.47
2225 2295 4.963318 TTTTGGGAATGGCAAATGTGTA 57.037 36.364 0.00 0.00 0.00 2.90
2228 2298 4.370094 ACATTTTGGGAATGGCAAATGT 57.630 36.364 5.80 5.80 42.40 2.71
2229 2299 6.092533 GTCTTACATTTTGGGAATGGCAAATG 59.907 38.462 0.00 0.00 40.81 2.32
2230 2300 6.013466 AGTCTTACATTTTGGGAATGGCAAAT 60.013 34.615 0.00 0.00 32.14 2.32
2232 2302 4.837860 AGTCTTACATTTTGGGAATGGCAA 59.162 37.500 0.00 0.00 32.14 4.52
2233 2303 4.415596 AGTCTTACATTTTGGGAATGGCA 58.584 39.130 0.00 0.00 32.14 4.92
2234 2304 6.507023 CATAGTCTTACATTTTGGGAATGGC 58.493 40.000 4.06 0.00 32.14 4.40
2236 2306 7.099266 TGCATAGTCTTACATTTTGGGAATG 57.901 36.000 0.00 0.00 0.00 2.67
2237 2307 7.716799 TTGCATAGTCTTACATTTTGGGAAT 57.283 32.000 0.00 0.00 0.00 3.01
2238 2308 7.716799 ATTGCATAGTCTTACATTTTGGGAA 57.283 32.000 0.00 0.00 0.00 3.97
2239 2309 8.995027 ATATTGCATAGTCTTACATTTTGGGA 57.005 30.769 0.00 0.00 0.00 4.37
2248 2318 9.599322 GCAAATGTGTATATTGCATAGTCTTAC 57.401 33.333 4.96 0.00 46.57 2.34
2258 2328 4.681025 CGGAATGGCAAATGTGTATATTGC 59.319 41.667 0.00 1.29 46.60 3.56
2259 2329 5.686841 CACGGAATGGCAAATGTGTATATTG 59.313 40.000 0.00 0.00 0.00 1.90
2260 2330 5.735922 GCACGGAATGGCAAATGTGTATATT 60.736 40.000 12.10 0.00 0.00 1.28
2263 2979 2.159254 GCACGGAATGGCAAATGTGTAT 60.159 45.455 12.10 0.00 0.00 2.29
2278 2994 2.747396 ACTTATTGTAACCGCACGGA 57.253 45.000 17.40 0.00 38.96 4.69
2314 3030 6.272318 TGCGATGATATTTGTTCCCATTTTC 58.728 36.000 0.00 0.00 0.00 2.29
2325 3042 6.908820 GCCATATGTACATGCGATGATATTTG 59.091 38.462 18.81 2.35 0.00 2.32
2350 3067 3.196039 TGAAAATGGGCAGATCCACATTG 59.804 43.478 0.82 0.00 39.97 2.82
2365 3082 4.459390 TTCATCAGTGCCCATGAAAATG 57.541 40.909 0.00 0.00 36.33 2.32
2375 3093 2.167075 CCCCTGAAATTTCATCAGTGCC 59.833 50.000 20.76 0.00 42.19 5.01
2377 3095 3.094572 AGCCCCTGAAATTTCATCAGTG 58.905 45.455 20.76 9.08 42.19 3.66
2379 3097 5.920193 TTTAGCCCCTGAAATTTCATCAG 57.080 39.130 20.76 9.75 43.15 2.90
2391 3109 5.634118 TGGAGATATGATTTTTAGCCCCTG 58.366 41.667 0.00 0.00 0.00 4.45
2408 3126 7.099266 TCGCATGAAATTAACAATTGGAGAT 57.901 32.000 10.83 0.00 0.00 2.75
2412 3130 6.034898 GGACTTCGCATGAAATTAACAATTGG 59.965 38.462 10.83 0.00 32.66 3.16
2427 3145 1.260538 TGAGAGGCAGGACTTCGCAT 61.261 55.000 0.00 0.00 0.00 4.73
2448 3166 1.281867 TGGTGGTAATTGCCTGAGAGG 59.718 52.381 14.11 0.00 38.80 3.69
2471 3189 6.848451 TCACTTAAGGCTTTTAAATTAGGCG 58.152 36.000 4.45 0.00 41.41 5.52
2472 3190 9.731819 GTATCACTTAAGGCTTTTAAATTAGGC 57.268 33.333 4.45 5.53 37.22 3.93
2480 3198 6.996282 GCCTATGGTATCACTTAAGGCTTTTA 59.004 38.462 4.45 0.00 37.01 1.52
2490 3208 3.260884 CGGGTATGCCTATGGTATCACTT 59.739 47.826 0.00 0.00 34.45 3.16
2491 3209 2.832129 CGGGTATGCCTATGGTATCACT 59.168 50.000 0.00 0.00 34.45 3.41
2524 3242 0.737367 CGATGCTGATGGTCACGTGT 60.737 55.000 16.51 0.00 0.00 4.49
2527 3245 0.371301 CAACGATGCTGATGGTCACG 59.629 55.000 0.00 0.00 0.00 4.35
2542 3260 6.861572 TCACTCTTCAGATACTGTAAACAACG 59.138 38.462 0.00 0.00 32.61 4.10
2553 3273 5.738783 GCCTCCAAGATCACTCTTCAGATAC 60.739 48.000 0.00 0.00 39.78 2.24
2581 3301 2.230660 AGTTCAGGCTGGTGCTAAAAC 58.769 47.619 15.73 9.62 39.59 2.43
2584 3304 1.271379 GGAAGTTCAGGCTGGTGCTAA 60.271 52.381 15.73 0.00 39.59 3.09
2653 3373 8.720562 CACCAAGAAAAAGTGAGTTTGATTTTT 58.279 29.630 0.00 0.00 37.51 1.94
2720 3440 4.220693 TGCTGTAACCTAATCACTGCAT 57.779 40.909 0.00 0.00 40.68 3.96


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

AutoCloner maintained by Alex Coulton.