Multiple sequence alignment - TraesCS1D01G192600

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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 TraesCS1D01G192600 chr1D 100.000 2669 0 0 1 2669 268939462 268936794 0.000000e+00 4929.0
1 TraesCS1D01G192600 chr1B 91.533 1807 74 33 417 2190 370044503 370046263 0.000000e+00 2416.0
2 TraesCS1D01G192600 chr1B 91.168 351 23 3 46 394 370044077 370044421 1.120000e-128 470.0
3 TraesCS1D01G192600 chr1B 91.815 281 12 3 2395 2669 370046638 370046913 5.390000e-102 381.0
4 TraesCS1D01G192600 chr1B 86.667 165 9 3 2186 2339 370046387 370046549 1.270000e-38 171.0
5 TraesCS1D01G192600 chr1A 90.345 1129 61 20 591 1689 333912949 333914059 0.000000e+00 1437.0
6 TraesCS1D01G192600 chr1A 88.745 542 22 13 1723 2242 333914066 333914590 6.270000e-176 627.0
7 TraesCS1D01G192600 chr1A 85.552 616 50 20 3 594 333912151 333912751 2.270000e-170 608.0
8 TraesCS1D01G192600 chr1A 87.004 277 12 3 2393 2669 333914741 333914993 9.350000e-75 291.0
9 TraesCS1D01G192600 chr1A 96.721 61 1 1 2275 2335 333914662 333914721 1.690000e-17 100.0
10 TraesCS1D01G192600 chr4A 91.133 203 10 2 17 211 628854945 628854743 4.380000e-68 268.0
11 TraesCS1D01G192600 chr7A 88.060 134 16 0 331 464 238551525 238551392 2.750000e-35 159.0
12 TraesCS1D01G192600 chr7A 86.131 137 13 5 330 464 580510030 580510162 2.770000e-30 143.0
13 TraesCS1D01G192600 chr3B 87.313 134 17 0 331 464 259702262 259702129 1.280000e-33 154.0
14 TraesCS1D01G192600 chr3B 85.821 134 19 0 331 464 358639807 358639674 2.770000e-30 143.0
15 TraesCS1D01G192600 chr5D 87.692 130 16 0 330 459 61714059 61713930 4.600000e-33 152.0
16 TraesCS1D01G192600 chr6A 87.407 135 12 4 330 464 151462178 151462049 1.660000e-32 150.0
17 TraesCS1D01G192600 chr6D 86.667 135 16 2 330 464 127200672 127200804 5.950000e-32 148.0
18 TraesCS1D01G192600 chr3D 86.466 133 18 0 331 463 286532915 286532783 2.140000e-31 147.0
19 TraesCS1D01G192600 chr4D 94.000 50 0 1 1118 1164 497627995 497627946 3.690000e-09 73.1


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 TraesCS1D01G192600 chr1D 268936794 268939462 2668 True 4929.0 4929 100.00000 1 2669 1 chr1D.!!$R1 2668
1 TraesCS1D01G192600 chr1B 370044077 370046913 2836 False 859.5 2416 90.29575 46 2669 4 chr1B.!!$F1 2623
2 TraesCS1D01G192600 chr1A 333912151 333914993 2842 False 612.6 1437 89.67340 3 2669 5 chr1A.!!$F1 2666

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
950 1259 0.179163 CTCACTCACGCGCATACTGA 60.179 55.0 5.73 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 2230 0.038599 ATTGATGAGCACAGCCCACA 59.961 50.0 0.0 0.0 0.0 4.17 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
38 43 6.807708 AGTAGATAGTGTTAATTGTTCGCG 57.192 37.500 0.00 0.00 0.00 5.87
42 47 5.808540 AGATAGTGTTAATTGTTCGCGCTTA 59.191 36.000 5.56 0.00 0.00 3.09
43 48 4.061570 AGTGTTAATTGTTCGCGCTTAC 57.938 40.909 5.56 3.56 0.00 2.34
55 60 6.037726 TGTTCGCGCTTACTTAGATTTATGA 58.962 36.000 5.56 0.00 0.00 2.15
191 200 2.062177 ACCCACCCGACTAATCCCG 61.062 63.158 0.00 0.00 0.00 5.14
192 201 2.108362 CCACCCGACTAATCCCGC 59.892 66.667 0.00 0.00 0.00 6.13
200 209 3.399330 CCGACTAATCCCGCATTATTGT 58.601 45.455 0.00 0.00 0.00 2.71
211 220 2.121786 GCATTATTGTTGGCTGCATCG 58.878 47.619 0.50 0.00 33.13 3.84
216 225 0.804364 TTGTTGGCTGCATCGATGAC 59.196 50.000 29.20 19.21 0.00 3.06
218 227 1.451927 TTGGCTGCATCGATGACCC 60.452 57.895 29.20 22.26 0.00 4.46
256 267 7.986085 TCTTTTGGGACTGAAAAAGAGATAG 57.014 36.000 6.51 0.00 43.80 2.08
402 423 8.773645 TCATGTCTTAGTGTATTTGTTCACTTG 58.226 33.333 3.25 0.00 43.39 3.16
406 427 9.434559 GTCTTAGTGTATTTGTTCACTTGTTTC 57.565 33.333 3.25 0.00 43.39 2.78
407 428 9.168451 TCTTAGTGTATTTGTTCACTTGTTTCA 57.832 29.630 3.25 0.00 43.39 2.69
408 429 9.221775 CTTAGTGTATTTGTTCACTTGTTTCAC 57.778 33.333 3.25 0.00 43.39 3.18
410 431 6.377146 AGTGTATTTGTTCACTTGTTTCACCT 59.623 34.615 0.00 0.00 41.33 4.00
421 501 5.345202 CACTTGTTTCACCTCGTATGTAGTC 59.655 44.000 0.00 0.00 0.00 2.59
479 571 2.277084 GGAGGTACACGATTTGCGAAT 58.723 47.619 0.00 0.00 44.57 3.34
480 572 2.030457 GGAGGTACACGATTTGCGAATG 59.970 50.000 3.20 0.00 44.57 2.67
481 573 2.671396 GAGGTACACGATTTGCGAATGT 59.329 45.455 3.20 0.00 44.57 2.71
482 574 2.415168 AGGTACACGATTTGCGAATGTG 59.585 45.455 19.39 19.39 44.57 3.21
483 575 2.413796 GGTACACGATTTGCGAATGTGA 59.586 45.455 24.21 12.53 44.57 3.58
484 576 3.063452 GGTACACGATTTGCGAATGTGAT 59.937 43.478 24.21 15.65 44.57 3.06
485 577 3.829886 ACACGATTTGCGAATGTGATT 57.170 38.095 24.21 9.64 44.57 2.57
486 578 3.747193 ACACGATTTGCGAATGTGATTC 58.253 40.909 24.21 4.94 44.57 2.52
487 579 3.436704 ACACGATTTGCGAATGTGATTCT 59.563 39.130 24.21 8.92 44.57 2.40
488 580 3.782369 CACGATTTGCGAATGTGATTCTG 59.218 43.478 17.52 0.68 44.57 3.02
489 581 3.436704 ACGATTTGCGAATGTGATTCTGT 59.563 39.130 3.20 0.00 44.57 3.41
490 582 4.083324 ACGATTTGCGAATGTGATTCTGTT 60.083 37.500 3.20 0.00 44.57 3.16
495 599 3.058293 TGCGAATGTGATTCTGTTTGACC 60.058 43.478 0.00 0.00 37.13 4.02
523 627 0.462375 AGCAACCTACGTGTGACACA 59.538 50.000 16.74 3.56 33.40 3.72
536 640 4.356405 TGTGACACATCCTCACAATTCT 57.644 40.909 3.56 0.00 43.99 2.40
604 909 6.240894 TCATCATTTTGGCCTATATCCACTC 58.759 40.000 3.32 0.00 32.45 3.51
619 927 7.891183 ATATCCACTCTACGATACAAAATGC 57.109 36.000 0.00 0.00 0.00 3.56
636 944 7.464358 ACAAAATGCACAGTATAATTCTCGAC 58.536 34.615 0.00 0.00 0.00 4.20
664 972 4.904895 TGGATGGAATTTTTCAATGGCA 57.095 36.364 0.00 0.00 0.00 4.92
716 1024 8.258708 AGTGAAAAGTACTATTCCTACATGGTC 58.741 37.037 0.00 0.00 37.07 4.02
717 1025 7.494952 GTGAAAAGTACTATTCCTACATGGTCC 59.505 40.741 0.00 0.00 37.07 4.46
719 1027 3.573110 AGTACTATTCCTACATGGTCCGC 59.427 47.826 0.00 0.00 37.07 5.54
828 1136 6.322491 CGGTCTGTTTGTTTCTTCTCTTTTT 58.678 36.000 0.00 0.00 0.00 1.94
839 1147 3.117888 TCTTCTCTTTTTCCACACAGCCT 60.118 43.478 0.00 0.00 0.00 4.58
945 1254 2.125912 GTCCTCACTCACGCGCAT 60.126 61.111 5.73 0.00 0.00 4.73
946 1255 1.138883 GTCCTCACTCACGCGCATA 59.861 57.895 5.73 0.00 0.00 3.14
947 1256 1.138883 TCCTCACTCACGCGCATAC 59.861 57.895 5.73 0.00 0.00 2.39
948 1257 1.139734 CCTCACTCACGCGCATACT 59.860 57.895 5.73 0.00 0.00 2.12
949 1258 1.142185 CCTCACTCACGCGCATACTG 61.142 60.000 5.73 0.00 0.00 2.74
950 1259 0.179163 CTCACTCACGCGCATACTGA 60.179 55.000 5.73 0.00 0.00 3.41
951 1260 0.179163 TCACTCACGCGCATACTGAG 60.179 55.000 18.76 18.76 37.93 3.35
952 1261 0.456824 CACTCACGCGCATACTGAGT 60.457 55.000 19.91 19.91 44.42 3.41
956 1265 1.153823 ACGCGCATACTGAGTCACC 60.154 57.895 5.73 0.00 0.00 4.02
977 1286 1.398958 ATCCAAGCCTCTCTCTCGCC 61.399 60.000 0.00 0.00 0.00 5.54
1218 1542 2.095252 GGCTGCCGAGTTCGACTTC 61.095 63.158 1.35 0.00 43.02 3.01
1263 1587 3.640407 TGCTTCTCCCCGCTGCTT 61.640 61.111 0.00 0.00 0.00 3.91
1518 1860 1.673665 GTCCAGGTCTGCTGCCTTG 60.674 63.158 0.00 2.47 33.31 3.61
1641 1983 4.685575 GCCATCCTCTACTGCAAGAAATCT 60.686 45.833 0.00 0.00 37.43 2.40
1690 2045 2.761195 GGCCGGCAAAAGATCGGTC 61.761 63.158 30.85 1.22 44.97 4.79
1698 2053 0.741221 AAAAGATCGGTCGCTGCTCC 60.741 55.000 0.00 0.00 0.00 4.70
1701 2056 1.880340 GATCGGTCGCTGCTCCTTG 60.880 63.158 0.00 0.00 0.00 3.61
1713 2068 3.102204 CTGCTCCTTGGGGATTTTGATT 58.898 45.455 0.00 0.00 41.36 2.57
1715 2070 3.099141 GCTCCTTGGGGATTTTGATTGA 58.901 45.455 0.00 0.00 41.36 2.57
1716 2071 3.708121 GCTCCTTGGGGATTTTGATTGAT 59.292 43.478 0.00 0.00 41.36 2.57
1727 2082 6.265577 GGATTTTGATTGATTTCCGGTGTAG 58.734 40.000 0.00 0.00 0.00 2.74
1741 2096 4.402474 TCCGGTGTAGATCCTATATGCATG 59.598 45.833 10.16 0.00 0.00 4.06
1745 2100 5.046304 GGTGTAGATCCTATATGCATGTGGT 60.046 44.000 10.16 0.16 0.00 4.16
1748 2103 5.683876 AGATCCTATATGCATGTGGTACC 57.316 43.478 10.16 4.43 0.00 3.34
1771 2126 6.073548 ACCTGAGTGTATAGCGTATACGTTAC 60.074 42.308 25.04 21.61 43.05 2.50
1780 2135 7.212782 GTATAGCGTATACGTTACGAAGTAAGC 59.787 40.741 25.04 13.65 43.33 3.09
1870 2230 2.899900 TGAAGCTACCTGTCACTGTCAT 59.100 45.455 0.00 0.00 0.00 3.06
1871 2231 3.257393 GAAGCTACCTGTCACTGTCATG 58.743 50.000 0.00 0.00 0.00 3.07
1872 2232 2.251818 AGCTACCTGTCACTGTCATGT 58.748 47.619 0.00 0.00 0.00 3.21
1873 2233 2.028658 AGCTACCTGTCACTGTCATGTG 60.029 50.000 0.00 0.00 39.15 3.21
1875 2235 0.397941 ACCTGTCACTGTCATGTGGG 59.602 55.000 0.00 0.00 38.40 4.61
1877 2237 0.035881 CTGTCACTGTCATGTGGGCT 59.964 55.000 0.00 0.00 38.40 5.19
1880 2240 0.250424 TCACTGTCATGTGGGCTGTG 60.250 55.000 0.00 0.00 38.40 3.66
1881 2241 1.601759 ACTGTCATGTGGGCTGTGC 60.602 57.895 0.00 0.00 0.00 4.57
1882 2242 1.303074 CTGTCATGTGGGCTGTGCT 60.303 57.895 0.00 0.00 0.00 4.40
1883 2243 1.302752 TGTCATGTGGGCTGTGCTC 60.303 57.895 0.00 0.00 0.00 4.26
1884 2244 1.302752 GTCATGTGGGCTGTGCTCA 60.303 57.895 0.00 0.00 36.30 4.26
1885 2245 0.679002 GTCATGTGGGCTGTGCTCAT 60.679 55.000 0.00 0.00 42.67 2.90
1886 2246 0.393402 TCATGTGGGCTGTGCTCATC 60.393 55.000 0.00 0.00 42.67 2.92
1887 2247 0.678684 CATGTGGGCTGTGCTCATCA 60.679 55.000 0.00 0.00 42.67 3.07
1888 2248 0.038599 ATGTGGGCTGTGCTCATCAA 59.961 50.000 0.00 0.00 42.67 2.57
1889 2249 0.038599 TGTGGGCTGTGCTCATCAAT 59.961 50.000 0.00 0.00 42.67 2.57
1890 2250 1.180029 GTGGGCTGTGCTCATCAATT 58.820 50.000 0.00 0.00 42.67 2.32
1891 2251 1.135199 GTGGGCTGTGCTCATCAATTG 60.135 52.381 0.00 0.00 42.67 2.32
1892 2252 1.180029 GGGCTGTGCTCATCAATTGT 58.820 50.000 5.13 0.00 0.00 2.71
1973 2333 6.432162 TCTCCTTCTAATTGCCATGATTATGC 59.568 38.462 0.00 0.00 32.79 3.14
2007 2375 0.538746 TATGCATGCATCAGGCCAGG 60.539 55.000 35.35 0.00 40.65 4.45
2086 2459 3.299503 AGCAAACTCATGTGTTTTCCCT 58.700 40.909 20.28 14.46 37.98 4.20
2204 2708 5.998454 AACATATAGCTGCACAGTTGATC 57.002 39.130 1.02 0.00 0.00 2.92
2257 2787 4.081807 GGGTAAGAGACATGTAGACCGTTT 60.082 45.833 0.00 0.00 0.00 3.60
2263 2793 5.007385 AGACATGTAGACCGTTTCATACC 57.993 43.478 0.00 0.00 0.00 2.73
2268 2798 3.444742 TGTAGACCGTTTCATACCGACAT 59.555 43.478 0.00 0.00 0.00 3.06
2325 2868 1.427020 GGCATCGAACTTGCAGAGC 59.573 57.895 11.32 0.00 41.95 4.09
2343 2886 6.200854 TGCAGAGCAATATCATTTGTACTACG 59.799 38.462 0.00 0.00 34.76 3.51
2345 2888 6.200854 CAGAGCAATATCATTTGTACTACGCA 59.799 38.462 0.00 0.00 0.00 5.24
2346 2889 6.422100 AGAGCAATATCATTTGTACTACGCAG 59.578 38.462 0.00 0.00 0.00 5.18
2350 2946 7.307989 GCAATATCATTTGTACTACGCAGGAAT 60.308 37.037 0.00 0.00 0.00 3.01
2355 2951 3.728076 TGTACTACGCAGGAATCATCC 57.272 47.619 0.00 0.00 46.98 3.51
2373 2969 1.386525 CCTGGCATGCAATTAGGCGT 61.387 55.000 21.36 0.00 36.28 5.68
2393 2989 3.381590 CGTGAGAGAGAGAGAGAGAGAGA 59.618 52.174 0.00 0.00 0.00 3.10
2394 2990 4.498850 CGTGAGAGAGAGAGAGAGAGAGAG 60.499 54.167 0.00 0.00 0.00 3.20
2395 2991 4.646945 GTGAGAGAGAGAGAGAGAGAGAGA 59.353 50.000 0.00 0.00 0.00 3.10
2396 2992 5.304101 GTGAGAGAGAGAGAGAGAGAGAGAT 59.696 48.000 0.00 0.00 0.00 2.75
2397 2993 6.491745 GTGAGAGAGAGAGAGAGAGAGAGATA 59.508 46.154 0.00 0.00 0.00 1.98
2398 2994 6.718912 TGAGAGAGAGAGAGAGAGAGAGATAG 59.281 46.154 0.00 0.00 0.00 2.08
2399 2995 6.857848 AGAGAGAGAGAGAGAGAGAGATAGA 58.142 44.000 0.00 0.00 0.00 1.98
2400 2996 6.947733 AGAGAGAGAGAGAGAGAGAGATAGAG 59.052 46.154 0.00 0.00 0.00 2.43
2401 2997 6.857848 AGAGAGAGAGAGAGAGAGATAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
2402 2998 6.947733 AGAGAGAGAGAGAGAGAGATAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
2403 2999 6.857848 AGAGAGAGAGAGAGAGATAGAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
2404 3000 6.947733 AGAGAGAGAGAGAGAGATAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
2405 3001 6.857848 AGAGAGAGAGAGAGATAGAGAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
2406 3002 6.947733 AGAGAGAGAGAGAGATAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
2407 3003 6.857848 AGAGAGAGAGAGATAGAGAGAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
2408 3004 6.947733 AGAGAGAGAGAGATAGAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
2409 3005 6.857848 AGAGAGAGAGATAGAGAGAGAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
2410 3006 6.947733 AGAGAGAGAGATAGAGAGAGAGAGAG 59.052 46.154 0.00 0.00 0.00 3.20
2435 3031 0.034756 CCGACATGGACTGTTCACCA 59.965 55.000 0.00 0.00 42.00 4.17
2445 3041 3.009723 GACTGTTCACCACCCATACATG 58.990 50.000 0.00 0.00 0.00 3.21
2546 3148 1.325476 GGTTGTCGTATCTCCCCGGT 61.325 60.000 0.00 0.00 0.00 5.28
2583 3185 2.125350 GACAGCTCTCCAAGGGCG 60.125 66.667 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.298774 GCGAACAATTAACACTATCTACTAGTT 57.701 33.333 0.00 0.00 38.68 2.24
12 13 7.642978 CGCGAACAATTAACACTATCTACTAGT 59.357 37.037 0.00 0.00 41.53 2.57
13 14 7.357368 GCGCGAACAATTAACACTATCTACTAG 60.357 40.741 12.10 0.00 0.00 2.57
14 15 6.415867 GCGCGAACAATTAACACTATCTACTA 59.584 38.462 12.10 0.00 0.00 1.82
15 16 5.231568 GCGCGAACAATTAACACTATCTACT 59.768 40.000 12.10 0.00 0.00 2.57
55 60 6.161381 GGAACAATGCTCAATGTTTTCAGAT 58.839 36.000 4.98 0.00 39.73 2.90
191 200 2.121786 CGATGCAGCCAACAATAATGC 58.878 47.619 0.00 0.00 37.40 3.56
192 201 3.696281 TCGATGCAGCCAACAATAATG 57.304 42.857 0.00 0.00 0.00 1.90
200 209 1.451927 GGGTCATCGATGCAGCCAA 60.452 57.895 26.93 9.00 0.00 4.52
256 267 6.705825 AGTGGGAAAGACAAATAACAAAATGC 59.294 34.615 0.00 0.00 0.00 3.56
375 396 9.507329 AAGTGAACAAATACACTAAGACATGAT 57.493 29.630 0.00 0.00 44.94 2.45
382 403 9.221775 GTGAAACAAGTGAACAAATACACTAAG 57.778 33.333 0.00 0.00 44.94 2.18
402 423 9.395707 CAATATAGACTACATACGAGGTGAAAC 57.604 37.037 0.00 0.00 0.00 2.78
447 533 3.365820 CGTGTACCTCCGTTCACAAATAC 59.634 47.826 0.00 0.00 39.53 1.89
479 571 8.231692 TCTAAATTTGGTCAAACAGAATCACA 57.768 30.769 0.00 0.00 32.51 3.58
480 572 7.327032 GCTCTAAATTTGGTCAAACAGAATCAC 59.673 37.037 0.00 0.00 32.51 3.06
481 573 7.014134 TGCTCTAAATTTGGTCAAACAGAATCA 59.986 33.333 0.00 2.08 32.51 2.57
482 574 7.370383 TGCTCTAAATTTGGTCAAACAGAATC 58.630 34.615 0.00 0.07 32.51 2.52
483 575 7.288810 TGCTCTAAATTTGGTCAAACAGAAT 57.711 32.000 0.00 0.00 32.51 2.40
484 576 6.707440 TGCTCTAAATTTGGTCAAACAGAA 57.293 33.333 0.00 0.00 32.51 3.02
485 577 6.460953 GGTTGCTCTAAATTTGGTCAAACAGA 60.461 38.462 16.12 3.73 32.51 3.41
486 578 5.691754 GGTTGCTCTAAATTTGGTCAAACAG 59.308 40.000 16.12 3.18 32.51 3.16
487 579 5.362430 AGGTTGCTCTAAATTTGGTCAAACA 59.638 36.000 20.03 5.79 32.51 2.83
488 580 5.842907 AGGTTGCTCTAAATTTGGTCAAAC 58.157 37.500 14.44 14.44 32.51 2.93
489 581 6.293735 CGTAGGTTGCTCTAAATTTGGTCAAA 60.294 38.462 0.00 0.00 34.46 2.69
490 582 5.180492 CGTAGGTTGCTCTAAATTTGGTCAA 59.820 40.000 0.00 4.68 0.00 3.18
495 599 5.178623 TCACACGTAGGTTGCTCTAAATTTG 59.821 40.000 0.00 0.00 0.00 2.32
523 627 1.740380 CGCCGACAGAATTGTGAGGAT 60.740 52.381 19.90 0.00 37.76 3.24
532 636 2.450609 AAACTACACGCCGACAGAAT 57.549 45.000 0.00 0.00 0.00 2.40
536 640 3.057386 TCATCTAAAACTACACGCCGACA 60.057 43.478 0.00 0.00 0.00 4.35
576 680 7.341256 GTGGATATAGGCCAAAATGATGATCAT 59.659 37.037 8.25 8.25 36.46 2.45
619 927 8.712363 CCAAATATGGTCGAGAATTATACTGTG 58.288 37.037 0.00 0.00 42.18 3.66
656 964 1.881973 GAGCAGACTGTTTGCCATTGA 59.118 47.619 18.39 0.00 42.48 2.57
702 1010 4.133820 CAATTGCGGACCATGTAGGAATA 58.866 43.478 0.00 0.00 41.22 1.75
703 1011 2.951642 CAATTGCGGACCATGTAGGAAT 59.048 45.455 0.00 0.00 41.22 3.01
704 1012 2.364632 CAATTGCGGACCATGTAGGAA 58.635 47.619 0.00 0.00 41.22 3.36
716 1024 1.228533 AAAAAGGCTTGCAATTGCGG 58.771 45.000 24.58 19.76 45.83 5.69
786 1094 0.318699 CGGTTGACGTCTCTGAAGCA 60.319 55.000 17.92 0.00 37.93 3.91
828 1136 1.610673 GAGGAGGAGGCTGTGTGGA 60.611 63.158 0.00 0.00 0.00 4.02
945 1254 1.476891 GCTTGGATCGGTGACTCAGTA 59.523 52.381 0.00 0.00 0.00 2.74
946 1255 0.247736 GCTTGGATCGGTGACTCAGT 59.752 55.000 0.00 0.00 0.00 3.41
947 1256 0.460987 GGCTTGGATCGGTGACTCAG 60.461 60.000 0.00 0.00 0.00 3.35
948 1257 0.904865 AGGCTTGGATCGGTGACTCA 60.905 55.000 0.00 0.00 0.00 3.41
949 1258 0.179097 GAGGCTTGGATCGGTGACTC 60.179 60.000 0.00 0.00 0.00 3.36
950 1259 0.616111 AGAGGCTTGGATCGGTGACT 60.616 55.000 0.00 0.00 0.00 3.41
951 1260 0.179097 GAGAGGCTTGGATCGGTGAC 60.179 60.000 0.00 0.00 0.00 3.67
952 1261 0.324738 AGAGAGGCTTGGATCGGTGA 60.325 55.000 0.00 0.00 0.00 4.02
956 1265 0.310543 CGAGAGAGAGGCTTGGATCG 59.689 60.000 0.00 0.00 0.00 3.69
1188 1512 2.107953 GCAGCCTCCTCGTCATCC 59.892 66.667 0.00 0.00 0.00 3.51
1641 1983 1.704641 CATCCTGTCGTCCCTGGATA 58.295 55.000 0.00 0.00 40.13 2.59
1677 2019 1.226128 GCAGCGACCGATCTTTTGC 60.226 57.895 0.00 0.00 0.00 3.68
1678 2020 0.371645 GAGCAGCGACCGATCTTTTG 59.628 55.000 0.00 0.00 0.00 2.44
1680 2022 1.153549 GGAGCAGCGACCGATCTTT 60.154 57.895 0.00 0.00 0.00 2.52
1681 2023 1.608717 AAGGAGCAGCGACCGATCTT 61.609 55.000 6.12 0.00 0.00 2.40
1698 2053 5.111293 CGGAAATCAATCAAAATCCCCAAG 58.889 41.667 0.00 0.00 0.00 3.61
1701 2056 3.450817 ACCGGAAATCAATCAAAATCCCC 59.549 43.478 9.46 0.00 0.00 4.81
1713 2068 6.351033 GCATATAGGATCTACACCGGAAATCA 60.351 42.308 9.46 0.00 0.00 2.57
1715 2070 5.483937 TGCATATAGGATCTACACCGGAAAT 59.516 40.000 9.46 0.00 0.00 2.17
1716 2071 4.836175 TGCATATAGGATCTACACCGGAAA 59.164 41.667 9.46 0.00 0.00 3.13
1727 2082 5.187772 TCAGGTACCACATGCATATAGGATC 59.812 44.000 15.94 8.96 28.67 3.36
1741 2096 2.686915 ACGCTATACACTCAGGTACCAC 59.313 50.000 15.94 0.00 0.00 4.16
1745 2100 5.541845 ACGTATACGCTATACACTCAGGTA 58.458 41.667 24.64 0.00 44.43 3.08
1748 2103 6.005885 CGTAACGTATACGCTATACACTCAG 58.994 44.000 24.64 8.84 44.43 3.35
1771 2126 4.032217 CACAGCTCATACTTGCTTACTTCG 59.968 45.833 0.00 0.00 37.44 3.79
1870 2230 0.038599 ATTGATGAGCACAGCCCACA 59.961 50.000 0.00 0.00 0.00 4.17
1871 2231 1.135199 CAATTGATGAGCACAGCCCAC 60.135 52.381 0.00 0.00 0.00 4.61
1872 2232 1.179152 CAATTGATGAGCACAGCCCA 58.821 50.000 0.00 0.00 0.00 5.36
1873 2233 1.180029 ACAATTGATGAGCACAGCCC 58.820 50.000 13.59 0.00 0.00 5.19
1875 2235 4.156556 TCCTTAACAATTGATGAGCACAGC 59.843 41.667 13.59 0.00 0.00 4.40
1877 2237 4.154015 CGTCCTTAACAATTGATGAGCACA 59.846 41.667 13.59 0.00 0.00 4.57
1880 2240 4.870426 TCTCGTCCTTAACAATTGATGAGC 59.130 41.667 13.59 0.00 39.57 4.26
1881 2241 7.515841 CGAATCTCGTCCTTAACAATTGATGAG 60.516 40.741 13.59 6.48 40.57 2.90
1882 2242 6.255670 CGAATCTCGTCCTTAACAATTGATGA 59.744 38.462 13.59 0.00 34.72 2.92
1883 2243 6.414079 CGAATCTCGTCCTTAACAATTGATG 58.586 40.000 13.59 0.00 34.72 3.07
1884 2244 5.523916 CCGAATCTCGTCCTTAACAATTGAT 59.476 40.000 13.59 2.25 38.40 2.57
1885 2245 4.868171 CCGAATCTCGTCCTTAACAATTGA 59.132 41.667 13.59 0.00 38.40 2.57
1886 2246 4.630069 ACCGAATCTCGTCCTTAACAATTG 59.370 41.667 3.24 3.24 38.40 2.32
1887 2247 4.828829 ACCGAATCTCGTCCTTAACAATT 58.171 39.130 0.00 0.00 38.40 2.32
1888 2248 4.467198 ACCGAATCTCGTCCTTAACAAT 57.533 40.909 0.00 0.00 38.40 2.71
1889 2249 3.947910 ACCGAATCTCGTCCTTAACAA 57.052 42.857 0.00 0.00 38.40 2.83
1890 2250 3.256383 TGAACCGAATCTCGTCCTTAACA 59.744 43.478 0.00 0.00 38.40 2.41
1891 2251 3.841643 TGAACCGAATCTCGTCCTTAAC 58.158 45.455 0.00 0.00 38.40 2.01
1892 2252 4.524316 TTGAACCGAATCTCGTCCTTAA 57.476 40.909 0.00 0.00 38.40 1.85
1973 2333 7.104326 TGCATGCATACATATATAATACGCG 57.896 36.000 18.46 3.53 33.67 6.01
2007 2375 1.819632 CCTAACGCATGGGGTCTGC 60.820 63.158 14.94 0.00 36.26 4.26
2098 2471 5.060940 GGTTTGAATGAGTTTTAGAATGCGC 59.939 40.000 0.00 0.00 0.00 6.09
2204 2708 4.585162 ACTGGACGACCTAGAAGATAATGG 59.415 45.833 5.33 0.00 37.04 3.16
2263 2793 2.030457 GGAAGATTGCACCGTAATGTCG 59.970 50.000 0.00 0.00 0.00 4.35
2268 2798 4.075682 TCATTTGGAAGATTGCACCGTAA 58.924 39.130 0.00 0.00 0.00 3.18
2325 2868 7.477144 TTCCTGCGTAGTACAAATGATATTG 57.523 36.000 0.00 0.00 36.37 1.90
2346 2889 1.405872 TTGCATGCCAGGATGATTCC 58.594 50.000 16.68 0.00 39.69 3.01
2350 2946 2.589720 CCTAATTGCATGCCAGGATGA 58.410 47.619 16.68 0.00 39.69 2.92
2355 2951 0.248743 CACGCCTAATTGCATGCCAG 60.249 55.000 16.68 6.96 0.00 4.85
2373 2969 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
2393 2989 6.325028 CGGATATCCTCTCTCTCTCTCTATCT 59.675 46.154 19.61 0.00 0.00 1.98
2394 2990 6.323996 TCGGATATCCTCTCTCTCTCTCTATC 59.676 46.154 19.61 0.00 0.00 2.08
2395 2991 6.098409 GTCGGATATCCTCTCTCTCTCTCTAT 59.902 46.154 19.61 0.00 0.00 1.98
2396 2992 5.421056 GTCGGATATCCTCTCTCTCTCTCTA 59.579 48.000 19.61 0.00 0.00 2.43
2397 2993 4.223032 GTCGGATATCCTCTCTCTCTCTCT 59.777 50.000 19.61 0.00 0.00 3.10
2398 2994 4.020573 TGTCGGATATCCTCTCTCTCTCTC 60.021 50.000 19.61 0.00 0.00 3.20
2399 2995 3.907474 TGTCGGATATCCTCTCTCTCTCT 59.093 47.826 19.61 0.00 0.00 3.10
2400 2996 4.280436 TGTCGGATATCCTCTCTCTCTC 57.720 50.000 19.61 0.88 0.00 3.20
2401 2997 4.567537 CCATGTCGGATATCCTCTCTCTCT 60.568 50.000 19.61 0.00 36.56 3.10
2402 2998 3.694072 CCATGTCGGATATCCTCTCTCTC 59.306 52.174 19.61 3.18 36.56 3.20
2403 2999 3.332187 TCCATGTCGGATATCCTCTCTCT 59.668 47.826 19.61 0.00 39.64 3.10
2404 3000 3.691575 TCCATGTCGGATATCCTCTCTC 58.308 50.000 19.61 6.00 39.64 3.20
2405 3001 3.816398 TCCATGTCGGATATCCTCTCT 57.184 47.619 19.61 0.00 39.64 3.10
2427 3023 2.505650 CCATGTATGGGTGGTGAACA 57.494 50.000 2.87 0.00 44.31 3.18
2499 3095 2.160219 CCATCCGATCACATTATTGGCG 59.840 50.000 0.00 0.00 31.24 5.69
2612 3214 2.102070 TGTCTCTCTCGGTCTCTGAC 57.898 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.