Multiple sequence alignment - TraesCS4D01G098000

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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 TraesCS4D01G098000 chr4D 100.000 2444 0 0 1 2444 74604940 74607383 0.000000e+00 4514.0
1 TraesCS4D01G098000 chr4B 90.342 2278 131 22 1 2209 106969252 106971509 0.000000e+00 2905.0
2 TraesCS4D01G098000 chr4B 83.834 433 60 7 1 424 672942967 672942536 1.050000e-108 403.0
3 TraesCS4D01G098000 chr4A 89.124 1747 92 32 766 2444 513090112 513088396 0.000000e+00 2084.0
4 TraesCS4D01G098000 chr4A 96.429 112 4 0 647 758 513090642 513090531 4.150000e-43 185.0
5 TraesCS4D01G098000 chr1D 84.848 429 57 6 1 421 444844603 444845031 2.250000e-115 425.0
6 TraesCS4D01G098000 chr1D 84.382 429 57 7 1 421 472292483 472292057 1.750000e-111 412.0
7 TraesCS4D01G098000 chr7D 84.722 432 57 5 1 424 635663657 635663227 8.080000e-115 424.0
8 TraesCS4D01G098000 chr3B 83.683 429 62 5 1 421 691284536 691284964 4.900000e-107 398.0
9 TraesCS4D01G098000 chr6A 83.488 430 61 7 1 421 497996322 497996750 2.280000e-105 392.0
10 TraesCS4D01G098000 chr2A 82.955 440 66 7 1 432 451014347 451014785 2.950000e-104 388.0
11 TraesCS4D01G098000 chr5B 83.063 431 65 5 2 424 679666782 679666352 3.810000e-103 385.0
12 TraesCS4D01G098000 chr5B 86.957 69 9 0 1136 1204 216392883 216392951 7.250000e-11 78.7
13 TraesCS4D01G098000 chr5D 86.957 69 9 0 1136 1204 193507385 193507453 7.250000e-11 78.7
14 TraesCS4D01G098000 chr5A 86.957 69 9 0 1136 1204 248536610 248536542 7.250000e-11 78.7


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 TraesCS4D01G098000 chr4D 74604940 74607383 2443 False 4514.0 4514 100.0000 1 2444 1 chr4D.!!$F1 2443
1 TraesCS4D01G098000 chr4B 106969252 106971509 2257 False 2905.0 2905 90.3420 1 2209 1 chr4B.!!$F1 2208
2 TraesCS4D01G098000 chr4A 513088396 513090642 2246 True 1134.5 2084 92.7765 647 2444 2 chr4A.!!$R1 1797

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
780 1208 0.335019 AGGTACCATGCCTTTTCCCC 59.665 55.0 15.94 0.0 31.04 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2604 0.610687 GATCATTAGGCCTCTCCCGG 59.389 60.0 9.68 0.0 34.51 5.73 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
32 33 5.581126 TCAATCATGGCCATACAAAGAAC 57.419 39.130 20.30 0.00 0.00 3.01
34 35 5.657745 TCAATCATGGCCATACAAAGAACAT 59.342 36.000 20.30 0.00 0.00 2.71
35 36 5.779529 ATCATGGCCATACAAAGAACATC 57.220 39.130 20.30 0.00 0.00 3.06
87 88 2.617532 GGACCACCTAGTGACGACTACT 60.618 54.545 0.00 0.00 35.23 2.57
103 104 3.626930 ACTACTAGCACTAGAGCAAGCT 58.373 45.455 14.80 8.82 40.92 3.74
107 108 2.091852 AGCACTAGAGCAAGCTGAAC 57.908 50.000 14.80 0.00 35.72 3.18
136 137 1.686110 GTCATCACCCCTCCCTCGT 60.686 63.158 0.00 0.00 0.00 4.18
164 165 3.624410 CCGGGCAAACCTTATTGTAGTAC 59.376 47.826 0.00 0.00 36.97 2.73
170 171 6.206048 GGCAAACCTTATTGTAGTACACAGTT 59.794 38.462 1.43 0.23 38.72 3.16
187 188 4.500477 CACAGTTGAAAAGTTGTGCTAAGC 59.500 41.667 0.00 0.00 36.31 3.09
197 199 0.837272 TGTGCTAAGCCCCATAGGAC 59.163 55.000 0.00 0.00 40.78 3.85
216 218 1.895231 CAGCACACCAGAGCAGCAA 60.895 57.895 0.00 0.00 33.43 3.91
222 224 0.607217 CACCAGAGCAGCAACCATCA 60.607 55.000 0.00 0.00 0.00 3.07
234 236 2.095718 GCAACCATCACCGAAGAAAGTC 60.096 50.000 0.00 0.00 0.00 3.01
235 237 3.138304 CAACCATCACCGAAGAAAGTCA 58.862 45.455 0.00 0.00 0.00 3.41
240 242 4.806247 CCATCACCGAAGAAAGTCATAGAC 59.194 45.833 0.00 0.00 0.00 2.59
241 243 4.451629 TCACCGAAGAAAGTCATAGACC 57.548 45.455 0.00 0.00 32.18 3.85
265 267 5.445939 CGGAAGGATCAAATCTGTAAACACG 60.446 44.000 0.00 0.00 0.00 4.49
270 272 5.342259 GGATCAAATCTGTAAACACGCAAAC 59.658 40.000 0.00 0.00 0.00 2.93
274 276 4.539509 ATCTGTAAACACGCAAACGAAA 57.460 36.364 0.00 0.00 43.93 3.46
275 277 3.930618 TCTGTAAACACGCAAACGAAAG 58.069 40.909 0.00 0.00 43.93 2.62
287 289 2.750301 AACGAAAGCGAACAAAGACC 57.250 45.000 0.00 0.00 41.64 3.85
312 314 4.387026 TCCAAACAGATCCACCAAAGAT 57.613 40.909 0.00 0.00 0.00 2.40
313 315 4.335416 TCCAAACAGATCCACCAAAGATC 58.665 43.478 0.00 0.00 40.42 2.75
314 316 3.127548 CCAAACAGATCCACCAAAGATCG 59.872 47.826 0.00 0.00 44.02 3.69
333 335 2.264480 CACCGACCGAATCCTGCA 59.736 61.111 0.00 0.00 0.00 4.41
339 341 1.212616 GACCGAATCCTGCAAGATCG 58.787 55.000 0.00 4.53 34.07 3.69
340 342 0.824109 ACCGAATCCTGCAAGATCGA 59.176 50.000 14.66 0.00 36.78 3.59
342 344 1.863454 CCGAATCCTGCAAGATCGAAG 59.137 52.381 14.66 2.20 36.78 3.79
365 368 3.626924 ACACCTCCACACGCCCTC 61.627 66.667 0.00 0.00 0.00 4.30
369 372 4.436998 CTCCACACGCCCTCCGAC 62.437 72.222 0.00 0.00 41.02 4.79
378 381 2.194212 GCCCTCCGACGATGCTAGA 61.194 63.158 0.00 0.00 0.00 2.43
394 397 0.733150 TAGACGCACCATCGAGACAG 59.267 55.000 0.00 0.00 0.00 3.51
395 398 1.213013 GACGCACCATCGAGACAGT 59.787 57.895 0.00 0.00 0.00 3.55
403 406 2.164624 ACCATCGAGACAGTGCTAGAAC 59.835 50.000 0.00 0.00 0.00 3.01
412 415 1.478510 CAGTGCTAGAACGTGGGAGAT 59.521 52.381 0.00 0.00 0.00 2.75
456 459 8.143835 ACCCATGTTTTCTTTTCTTTATGTCTG 58.856 33.333 0.00 0.00 0.00 3.51
616 619 2.128771 GCCTAAAAGCCCATCAGACA 57.871 50.000 0.00 0.00 0.00 3.41
624 641 1.117150 GCCCATCAGACATGGCAATT 58.883 50.000 0.00 0.00 43.46 2.32
633 650 3.189080 CAGACATGGCAATTTTCGTCAGA 59.811 43.478 0.00 0.00 0.00 3.27
720 737 2.019249 GCATCATCACTTGCTTAGCCA 58.981 47.619 0.29 0.00 35.95 4.75
758 775 1.827789 TTCTGGCCAACCACAGCAC 60.828 57.895 7.01 0.00 42.67 4.40
759 776 3.297620 CTGGCCAACCACAGCACC 61.298 66.667 7.01 0.00 42.67 5.01
763 780 2.598394 CCAACCACAGCACCCAGG 60.598 66.667 0.00 0.00 0.00 4.45
764 781 2.195683 CAACCACAGCACCCAGGT 59.804 61.111 0.00 0.00 35.47 4.00
780 1208 0.335019 AGGTACCATGCCTTTTCCCC 59.665 55.000 15.94 0.00 31.04 4.81
841 1269 3.496331 ACCGTCCATGAAGGTGAAATTT 58.504 40.909 0.80 0.00 42.37 1.82
846 1274 6.458751 CCGTCCATGAAGGTGAAATTTATGAG 60.459 42.308 0.00 0.00 39.02 2.90
851 1279 7.775093 CCATGAAGGTGAAATTTATGAGACCTA 59.225 37.037 0.00 0.00 32.52 3.08
861 1289 8.747538 AAATTTATGAGACCTACATTACCACC 57.252 34.615 0.00 0.00 0.00 4.61
864 1292 3.786553 TGAGACCTACATTACCACCACT 58.213 45.455 0.00 0.00 0.00 4.00
868 1296 2.027192 ACCTACATTACCACCACTGCTG 60.027 50.000 0.00 0.00 0.00 4.41
896 1330 6.983307 ACACGTACCTCATAGTACTGTACTAG 59.017 42.308 26.37 17.61 43.85 2.57
897 1331 7.147828 ACACGTACCTCATAGTACTGTACTAGA 60.148 40.741 26.37 21.59 43.85 2.43
898 1332 7.168972 CACGTACCTCATAGTACTGTACTAGAC 59.831 44.444 26.37 17.08 43.85 2.59
899 1333 7.069331 ACGTACCTCATAGTACTGTACTAGACT 59.931 40.741 26.37 12.24 43.85 3.24
914 1348 8.049165 TGTACTAGACTACCACCTCCATATAA 57.951 38.462 0.00 0.00 0.00 0.98
916 1350 9.531158 GTACTAGACTACCACCTCCATATAAAT 57.469 37.037 0.00 0.00 0.00 1.40
945 1379 5.926663 TCTAGTGGTCGACAGATACATACT 58.073 41.667 18.91 9.81 0.00 2.12
946 1380 7.059202 TCTAGTGGTCGACAGATACATACTA 57.941 40.000 18.91 10.35 0.00 1.82
947 1381 6.927936 TCTAGTGGTCGACAGATACATACTAC 59.072 42.308 18.91 0.00 0.00 2.73
948 1382 5.434408 AGTGGTCGACAGATACATACTACA 58.566 41.667 18.91 0.00 0.00 2.74
1029 1482 0.696143 TCACTTTCCCCACTGTCCCA 60.696 55.000 0.00 0.00 0.00 4.37
1263 1728 1.375326 GAAGGAGGCCGAGTGGTTT 59.625 57.895 0.00 0.00 37.67 3.27
1422 1887 3.710209 CTGGTCAAGAAGTCCAGGAAT 57.290 47.619 0.00 0.00 46.05 3.01
1445 1910 1.091771 AGAACCGCGCCAATCTGATG 61.092 55.000 0.00 0.00 0.00 3.07
1447 1912 0.676466 AACCGCGCCAATCTGATGAA 60.676 50.000 0.00 0.00 0.00 2.57
1468 1933 3.630892 ATCAGATGAGCTGCAGAAGTT 57.369 42.857 20.43 0.00 44.52 2.66
1557 2039 7.393551 ACATGTGTAATTTTGCTTTTTCTCG 57.606 32.000 0.00 0.00 0.00 4.04
1586 2068 5.297029 ACTTCTTTTTGGCTGAAGAGTGTAC 59.703 40.000 8.65 0.00 39.42 2.90
1686 2171 8.884124 TTGTTTTTCCCTCTGAATCATCTAAT 57.116 30.769 0.00 0.00 31.67 1.73
1710 2195 6.798315 TTTTGGTTTTGTATGGAATGCATG 57.202 33.333 0.00 0.00 39.17 4.06
1714 2199 5.011431 TGGTTTTGTATGGAATGCATGACAA 59.989 36.000 0.00 3.75 39.17 3.18
1726 2211 6.867816 GGAATGCATGACAAGTTTATCAACAA 59.132 34.615 0.00 0.00 35.05 2.83
1738 2223 8.446273 CAAGTTTATCAACAACACTAGGATGAG 58.554 37.037 0.00 0.00 35.05 2.90
1780 2266 5.128205 TGGACATTGCTCTTCCATTATCTG 58.872 41.667 0.00 0.00 34.35 2.90
1885 2371 1.204704 CACCAACCTCGTAGATGCAGA 59.795 52.381 0.00 0.00 33.89 4.26
1886 2372 2.111384 ACCAACCTCGTAGATGCAGAT 58.889 47.619 0.00 0.00 33.89 2.90
1887 2373 2.159043 ACCAACCTCGTAGATGCAGATG 60.159 50.000 0.00 0.00 33.89 2.90
1888 2374 1.863454 CAACCTCGTAGATGCAGATGC 59.137 52.381 0.00 0.00 42.50 3.91
1955 2441 3.645975 CGGCACCGTCACCAACAC 61.646 66.667 0.00 0.00 34.35 3.32
1961 2447 1.147376 CCGTCACCAACACCTCCAA 59.853 57.895 0.00 0.00 0.00 3.53
1991 2477 0.465460 AAGCAGAAAACCAGACGCCA 60.465 50.000 0.00 0.00 0.00 5.69
1992 2478 0.465460 AGCAGAAAACCAGACGCCAA 60.465 50.000 0.00 0.00 0.00 4.52
1993 2479 0.383949 GCAGAAAACCAGACGCCAAA 59.616 50.000 0.00 0.00 0.00 3.28
1994 2480 1.600413 GCAGAAAACCAGACGCCAAAG 60.600 52.381 0.00 0.00 0.00 2.77
1995 2481 1.676006 CAGAAAACCAGACGCCAAAGT 59.324 47.619 0.00 0.00 0.00 2.66
1996 2482 1.947456 AGAAAACCAGACGCCAAAGTC 59.053 47.619 0.00 0.00 41.23 3.01
2039 2529 5.101628 CACTTAACAACACACTGCAACAAT 58.898 37.500 0.00 0.00 0.00 2.71
2043 2533 2.754552 ACAACACACTGCAACAATCACT 59.245 40.909 0.00 0.00 0.00 3.41
2109 2604 2.077842 ATCCCCTGCCTGATGATGCC 62.078 60.000 0.00 0.00 0.00 4.40
2110 2605 2.203451 CCCTGCCTGATGATGCCC 60.203 66.667 0.00 0.00 0.00 5.36
2111 2606 2.593725 CCTGCCTGATGATGCCCG 60.594 66.667 0.00 0.00 0.00 6.13
2112 2607 2.593725 CTGCCTGATGATGCCCGG 60.594 66.667 0.00 0.00 0.00 5.73
2113 2608 4.193893 TGCCTGATGATGCCCGGG 62.194 66.667 19.09 19.09 0.00 5.73
2114 2609 3.877450 GCCTGATGATGCCCGGGA 61.877 66.667 29.31 10.35 0.00 5.14
2115 2610 2.429058 CCTGATGATGCCCGGGAG 59.571 66.667 29.31 10.87 0.00 4.30
2116 2611 2.142761 CCTGATGATGCCCGGGAGA 61.143 63.158 29.31 10.55 0.00 3.71
2117 2612 1.370437 CTGATGATGCCCGGGAGAG 59.630 63.158 29.31 3.93 0.00 3.20
2118 2613 2.109517 CTGATGATGCCCGGGAGAGG 62.110 65.000 29.31 0.00 0.00 3.69
2134 2629 3.401182 GAGAGGCCTAATGATCTTGCTG 58.599 50.000 4.42 0.00 0.00 4.41
2135 2630 3.044156 AGAGGCCTAATGATCTTGCTGA 58.956 45.455 4.42 0.00 0.00 4.26
2146 2641 3.385755 TGATCTTGCTGAGCATGCTACTA 59.614 43.478 22.74 9.40 38.76 1.82
2147 2642 3.893326 TCTTGCTGAGCATGCTACTAA 57.107 42.857 22.74 12.45 38.76 2.24
2148 2643 4.412796 TCTTGCTGAGCATGCTACTAAT 57.587 40.909 22.74 0.00 38.76 1.73
2279 2782 9.862371 AGTACAAAGAAGTCAATCATAGTACAG 57.138 33.333 0.00 0.00 32.73 2.74
2295 2798 5.408880 AGTACAGAACTCCCTTAGAAAGC 57.591 43.478 0.00 0.00 30.33 3.51
2297 2800 3.252351 ACAGAACTCCCTTAGAAAGCCT 58.748 45.455 0.00 0.00 0.00 4.58
2315 2818 5.096443 AGCCTCTTTGATCAAGACCTTAG 57.904 43.478 8.41 2.28 36.51 2.18
2320 2823 6.593382 CCTCTTTGATCAAGACCTTAGAAGTG 59.407 42.308 8.41 1.35 36.51 3.16
2321 2824 7.303182 TCTTTGATCAAGACCTTAGAAGTGA 57.697 36.000 8.41 0.00 36.51 3.41
2331 2834 7.368198 AGACCTTAGAAGTGAGAGACTTTTT 57.632 36.000 0.00 0.00 45.48 1.94
2332 2835 7.438564 AGACCTTAGAAGTGAGAGACTTTTTC 58.561 38.462 0.00 0.00 45.48 2.29
2335 2838 4.939052 AGAAGTGAGAGACTTTTTCGGA 57.061 40.909 0.00 0.00 45.48 4.55
2379 2882 0.248661 CTGTCACGATCTGGCCTACG 60.249 60.000 3.32 7.10 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.131264 TCTTTGTATGGCCATGATTGAAGAT 58.869 36.000 29.04 0.13 0.00 2.40
19 20 7.792374 TTATCTCTGATGTTCTTTGTATGGC 57.208 36.000 0.00 0.00 0.00 4.40
87 88 2.416027 CGTTCAGCTTGCTCTAGTGCTA 60.416 50.000 17.08 9.28 34.10 3.49
116 117 2.365635 AGGGAGGGGTGATGACGG 60.366 66.667 0.00 0.00 0.00 4.79
117 118 2.786495 CGAGGGAGGGGTGATGACG 61.786 68.421 0.00 0.00 0.00 4.35
164 165 4.500477 GCTTAGCACAACTTTTCAACTGTG 59.500 41.667 0.00 0.00 41.68 3.66
170 171 1.960689 GGGGCTTAGCACAACTTTTCA 59.039 47.619 9.28 0.00 30.93 2.69
178 179 0.837272 GTCCTATGGGGCTTAGCACA 59.163 55.000 9.28 6.02 30.93 4.57
187 188 1.224592 GTGTGCTGGTCCTATGGGG 59.775 63.158 0.00 0.00 0.00 4.96
197 199 3.054503 GCTGCTCTGGTGTGCTGG 61.055 66.667 0.00 0.00 33.98 4.85
216 218 3.703001 ATGACTTTCTTCGGTGATGGT 57.297 42.857 0.00 0.00 0.00 3.55
222 224 2.165845 CCGGTCTATGACTTTCTTCGGT 59.834 50.000 0.00 0.00 32.47 4.69
234 236 4.993584 CAGATTTGATCCTTCCGGTCTATG 59.006 45.833 0.00 0.00 0.00 2.23
235 237 4.656112 ACAGATTTGATCCTTCCGGTCTAT 59.344 41.667 0.00 0.00 0.00 1.98
240 242 4.941263 TGTTTACAGATTTGATCCTTCCGG 59.059 41.667 0.00 0.00 0.00 5.14
241 243 5.445939 CGTGTTTACAGATTTGATCCTTCCG 60.446 44.000 0.00 0.00 0.00 4.30
249 251 4.034163 TCGTTTGCGTGTTTACAGATTTGA 59.966 37.500 0.00 0.00 39.49 2.69
254 256 3.786161 GCTTTCGTTTGCGTGTTTACAGA 60.786 43.478 0.00 0.00 39.49 3.41
255 257 2.462565 GCTTTCGTTTGCGTGTTTACAG 59.537 45.455 0.00 0.00 39.49 2.74
265 267 2.213353 GTCTTTGTTCGCTTTCGTTTGC 59.787 45.455 0.00 0.00 36.96 3.68
270 272 0.110823 CCGGTCTTTGTTCGCTTTCG 60.111 55.000 0.00 0.00 0.00 3.46
274 276 0.391263 GGATCCGGTCTTTGTTCGCT 60.391 55.000 0.00 0.00 0.00 4.93
275 277 0.672401 TGGATCCGGTCTTTGTTCGC 60.672 55.000 7.39 0.00 0.00 4.70
314 316 2.511600 CAGGATTCGGTCGGTGCC 60.512 66.667 0.00 0.00 0.00 5.01
327 329 1.478510 GTCTCCTTCGATCTTGCAGGA 59.521 52.381 0.00 0.00 34.15 3.86
330 332 1.618343 TGTGTCTCCTTCGATCTTGCA 59.382 47.619 0.00 0.00 0.00 4.08
333 335 2.494073 GAGGTGTGTCTCCTTCGATCTT 59.506 50.000 0.00 0.00 35.20 2.40
378 381 1.080501 CACTGTCTCGATGGTGCGT 60.081 57.895 0.00 0.00 0.00 5.24
394 397 1.204941 ACATCTCCCACGTTCTAGCAC 59.795 52.381 0.00 0.00 0.00 4.40
395 398 1.557099 ACATCTCCCACGTTCTAGCA 58.443 50.000 0.00 0.00 0.00 3.49
397 400 5.290386 GGAATAACATCTCCCACGTTCTAG 58.710 45.833 0.00 0.00 0.00 2.43
412 415 1.829222 GGTCTCTCGGTGGGAATAACA 59.171 52.381 0.00 0.00 0.00 2.41
421 424 2.076863 GAAAACATGGGTCTCTCGGTG 58.923 52.381 0.00 0.00 0.00 4.94
456 459 5.743872 CGCAGGAAAAGCAAAGGAATTATAC 59.256 40.000 0.00 0.00 0.00 1.47
576 579 1.421646 CCCTTCTCCAACACAGGACTT 59.578 52.381 0.00 0.00 33.19 3.01
610 613 3.145286 TGACGAAAATTGCCATGTCTGA 58.855 40.909 0.00 0.00 0.00 3.27
612 615 3.411446 TCTGACGAAAATTGCCATGTCT 58.589 40.909 0.00 0.00 0.00 3.41
613 616 3.426695 CCTCTGACGAAAATTGCCATGTC 60.427 47.826 0.00 0.00 0.00 3.06
616 619 3.071874 TCCTCTGACGAAAATTGCCAT 57.928 42.857 0.00 0.00 0.00 4.40
624 641 0.249699 TTGCGCTTCCTCTGACGAAA 60.250 50.000 9.73 0.00 0.00 3.46
633 650 4.385405 AGCTCGCTTGCGCTTCCT 62.385 61.111 9.73 1.06 38.13 3.36
720 737 6.347696 CAGAACTAAGCTTCAAGAGATGGAT 58.652 40.000 0.00 0.00 0.00 3.41
758 775 1.474330 GAAAAGGCATGGTACCTGGG 58.526 55.000 14.36 3.55 37.67 4.45
759 776 1.474330 GGAAAAGGCATGGTACCTGG 58.526 55.000 14.36 6.23 37.67 4.45
763 780 1.663379 GCGGGGAAAAGGCATGGTAC 61.663 60.000 0.00 0.00 0.00 3.34
764 781 1.379309 GCGGGGAAAAGGCATGGTA 60.379 57.895 0.00 0.00 0.00 3.25
780 1208 5.696822 TCTAGTACTAAACTGAACTGTGCG 58.303 41.667 3.76 0.00 39.39 5.34
841 1269 5.362717 CAGTGGTGGTAATGTAGGTCTCATA 59.637 44.000 0.00 0.00 0.00 2.15
846 1274 2.236395 AGCAGTGGTGGTAATGTAGGTC 59.764 50.000 0.00 0.00 30.68 3.85
851 1279 3.650647 CCAGCAGTGGTGGTAATGT 57.349 52.632 29.49 0.00 45.06 2.71
868 1296 8.112854 AGTACAGTACTATGAGGTACGTGTACC 61.113 44.444 19.29 19.29 44.49 3.34
889 1323 4.875578 ATGGAGGTGGTAGTCTAGTACA 57.124 45.455 0.00 0.00 0.00 2.90
890 1324 8.930846 TTTATATGGAGGTGGTAGTCTAGTAC 57.069 38.462 0.00 0.00 0.00 2.73
914 1348 6.961360 TCTGTCGACCACTAGATTCATATT 57.039 37.500 14.12 0.00 0.00 1.28
916 1350 6.996282 TGTATCTGTCGACCACTAGATTCATA 59.004 38.462 18.03 1.76 32.54 2.15
924 1358 6.481313 GTGTAGTATGTATCTGTCGACCACTA 59.519 42.308 14.12 4.99 0.00 2.74
945 1379 5.628200 GCAAATCCCTATGGTGTAGTGTGTA 60.628 44.000 0.00 0.00 0.00 2.90
946 1380 4.843728 CAAATCCCTATGGTGTAGTGTGT 58.156 43.478 0.00 0.00 0.00 3.72
947 1381 3.627577 GCAAATCCCTATGGTGTAGTGTG 59.372 47.826 0.00 0.00 0.00 3.82
948 1382 3.265737 TGCAAATCCCTATGGTGTAGTGT 59.734 43.478 0.00 0.00 0.00 3.55
1263 1728 4.764336 CCGTCGCCGTCGCTGTAA 62.764 66.667 0.00 0.00 35.26 2.41
1422 1887 3.969250 GATTGGCGCGGTTCTCCCA 62.969 63.158 8.83 1.70 0.00 4.37
1445 1910 3.940221 ACTTCTGCAGCTCATCTGATTTC 59.060 43.478 9.47 0.00 45.72 2.17
1447 1912 3.630892 ACTTCTGCAGCTCATCTGATT 57.369 42.857 9.47 0.00 45.72 2.57
1460 1925 7.761249 ACCAATAATTTCTGCATTAACTTCTGC 59.239 33.333 0.00 0.00 38.87 4.26
1468 1933 5.356751 AGTCGCACCAATAATTTCTGCATTA 59.643 36.000 0.00 0.00 0.00 1.90
1557 2039 3.715628 TCAGCCAAAAAGAAGTCTTGC 57.284 42.857 0.00 0.00 36.12 4.01
1586 2068 8.834465 TCAAAACAAGAGAAAGATGAAGAAGAG 58.166 33.333 0.00 0.00 0.00 2.85
1686 2171 6.994496 TCATGCATTCCATACAAAACCAAAAA 59.006 30.769 0.00 0.00 31.47 1.94
1698 2183 7.878547 TGATAAACTTGTCATGCATTCCATA 57.121 32.000 0.00 0.00 31.47 2.74
1701 2186 6.389091 TGTTGATAAACTTGTCATGCATTCC 58.611 36.000 0.00 0.00 0.00 3.01
1702 2187 7.381948 TGTTGTTGATAAACTTGTCATGCATTC 59.618 33.333 0.00 0.00 0.00 2.67
1704 2189 6.642131 GTGTTGTTGATAAACTTGTCATGCAT 59.358 34.615 0.00 0.00 0.00 3.96
1710 2195 7.724305 TCCTAGTGTTGTTGATAAACTTGTC 57.276 36.000 0.00 0.00 0.00 3.18
1714 2199 7.604164 CACTCATCCTAGTGTTGTTGATAAACT 59.396 37.037 0.00 0.00 41.63 2.66
1726 2211 4.604156 TGTGATCTCACTCATCCTAGTGT 58.396 43.478 11.35 0.00 45.78 3.55
1738 2223 4.508124 GTCCATACGGAATTGTGATCTCAC 59.492 45.833 3.34 3.34 45.20 3.51
1780 2266 5.679734 TGCTTCAGTCACAAAGAAAGATC 57.320 39.130 0.00 0.00 0.00 2.75
1887 2373 2.825387 TGATGGCGATGCACCTGC 60.825 61.111 0.00 0.00 42.50 4.85
1888 2374 2.184830 CCTGATGGCGATGCACCTG 61.185 63.158 0.00 0.00 0.00 4.00
1889 2375 1.913951 TTCCTGATGGCGATGCACCT 61.914 55.000 0.00 0.00 0.00 4.00
1890 2376 1.451927 TTCCTGATGGCGATGCACC 60.452 57.895 0.00 0.00 0.00 5.01
1955 2441 1.572085 CTTCACGTGCTGCTTGGAGG 61.572 60.000 11.67 0.00 0.00 4.30
1961 2447 0.815213 TTTCTGCTTCACGTGCTGCT 60.815 50.000 24.89 0.00 0.00 4.24
1991 2477 6.865205 GCAACATTTATGAAGCTGAAGACTTT 59.135 34.615 0.00 0.00 0.00 2.66
1992 2478 6.016024 TGCAACATTTATGAAGCTGAAGACTT 60.016 34.615 0.00 0.00 34.20 3.01
1993 2479 5.474532 TGCAACATTTATGAAGCTGAAGACT 59.525 36.000 0.00 0.00 34.20 3.24
1994 2480 5.570589 GTGCAACATTTATGAAGCTGAAGAC 59.429 40.000 0.00 0.00 36.32 3.01
1995 2481 5.474532 AGTGCAACATTTATGAAGCTGAAGA 59.525 36.000 0.00 0.00 41.43 2.87
1996 2482 5.706916 AGTGCAACATTTATGAAGCTGAAG 58.293 37.500 0.00 0.00 41.43 3.02
1997 2483 5.710513 AGTGCAACATTTATGAAGCTGAA 57.289 34.783 0.00 0.00 41.43 3.02
1998 2484 5.710513 AAGTGCAACATTTATGAAGCTGA 57.289 34.783 0.00 0.00 41.43 4.26
2039 2529 2.182827 CCCTGATGTGAGAGGAAGTGA 58.817 52.381 0.00 0.00 0.00 3.41
2043 2533 1.902508 GTGACCCTGATGTGAGAGGAA 59.097 52.381 0.00 0.00 0.00 3.36
2095 2590 2.593725 CCGGGCATCATCAGGCAG 60.594 66.667 0.00 0.00 0.00 4.85
2109 2604 0.610687 GATCATTAGGCCTCTCCCGG 59.389 60.000 9.68 0.00 34.51 5.73
2110 2605 1.638529 AGATCATTAGGCCTCTCCCG 58.361 55.000 9.68 0.00 34.51 5.14
2111 2606 2.551938 GCAAGATCATTAGGCCTCTCCC 60.552 54.545 9.68 0.00 34.51 4.30
2112 2607 2.371510 AGCAAGATCATTAGGCCTCTCC 59.628 50.000 9.68 0.00 0.00 3.71
2113 2608 3.070734 TCAGCAAGATCATTAGGCCTCTC 59.929 47.826 9.68 0.00 0.00 3.20
2114 2609 3.044156 TCAGCAAGATCATTAGGCCTCT 58.956 45.455 9.68 0.00 0.00 3.69
2115 2610 3.401182 CTCAGCAAGATCATTAGGCCTC 58.599 50.000 9.68 0.00 0.00 4.70
2116 2611 2.486907 GCTCAGCAAGATCATTAGGCCT 60.487 50.000 11.78 11.78 0.00 5.19
2117 2612 1.878734 GCTCAGCAAGATCATTAGGCC 59.121 52.381 0.00 0.00 0.00 5.19
2118 2613 2.569059 TGCTCAGCAAGATCATTAGGC 58.431 47.619 0.00 0.00 34.76 3.93
2134 2629 5.059161 TGTGATTGGATTAGTAGCATGCTC 58.941 41.667 26.57 15.83 29.76 4.26
2135 2630 5.039920 TGTGATTGGATTAGTAGCATGCT 57.960 39.130 25.99 25.99 33.55 3.79
2146 2641 4.030216 GGTGGGGTTATTGTGATTGGATT 58.970 43.478 0.00 0.00 0.00 3.01
2147 2642 3.272020 AGGTGGGGTTATTGTGATTGGAT 59.728 43.478 0.00 0.00 0.00 3.41
2148 2643 2.652348 AGGTGGGGTTATTGTGATTGGA 59.348 45.455 0.00 0.00 0.00 3.53
2185 2680 7.012704 CAGGTTAATTGATCAGGACAATAGGTG 59.987 40.741 0.00 0.00 37.04 4.00
2279 2782 4.561500 AAGAGGCTTTCTAAGGGAGTTC 57.438 45.455 0.00 0.00 34.14 3.01
2295 2798 6.593382 CACTTCTAAGGTCTTGATCAAAGAGG 59.407 42.308 9.88 10.69 45.69 3.69
2297 2800 7.233553 TCTCACTTCTAAGGTCTTGATCAAAGA 59.766 37.037 9.88 5.43 42.83 2.52
2315 2818 3.741856 GGTCCGAAAAAGTCTCTCACTTC 59.258 47.826 0.00 0.00 45.32 3.01
2320 2823 2.059541 CGTGGTCCGAAAAAGTCTCTC 58.940 52.381 0.00 0.00 39.56 3.20
2321 2824 1.872653 GCGTGGTCCGAAAAAGTCTCT 60.873 52.381 0.00 0.00 39.56 3.10
2355 2858 1.071605 GCCAGATCGTGACAGAACAC 58.928 55.000 0.00 0.00 37.42 3.32
2361 2864 1.807226 CGTAGGCCAGATCGTGACA 59.193 57.895 5.01 0.00 0.00 3.58
2394 2897 1.001048 TCACTTGGTCGGTTACAGACG 60.001 52.381 9.30 0.00 39.38 4.18


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

AutoCloner maintained by Alex Coulton.