Multiple sequence alignment - TraesCS1A01G225800

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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 TraesCS1A01G225800 chr1A 100.000 2435 0 0 1 2435 396261347 396263781 0.000000e+00 4497.0
1 TraesCS1A01G225800 chr1A 83.718 694 77 21 932 1604 396283009 396283687 7.390000e-175 623.0
2 TraesCS1A01G225800 chr1A 80.138 725 85 32 932 1608 396285662 396286375 1.010000e-133 486.0
3 TraesCS1A01G225800 chr1A 86.111 432 59 1 332 763 491376011 491376441 4.740000e-127 464.0
4 TraesCS1A01G225800 chr1D 93.072 1328 71 15 757 2077 315616566 315617879 0.000000e+00 1923.0
5 TraesCS1A01G225800 chr1D 87.353 680 61 16 2 677 315615268 315615926 0.000000e+00 756.0
6 TraesCS1A01G225800 chr1D 82.148 717 85 27 932 1608 315643316 315644029 2.100000e-160 575.0
7 TraesCS1A01G225800 chr1D 82.583 689 79 20 932 1604 315640240 315640903 9.770000e-159 569.0
8 TraesCS1A01G225800 chr1B 92.164 855 43 9 817 1652 427522872 427523721 0.000000e+00 1186.0
9 TraesCS1A01G225800 chr1B 88.048 912 75 11 1176 2077 427771178 427772065 0.000000e+00 1050.0
10 TraesCS1A01G225800 chr1B 84.993 713 71 23 914 1604 427543028 427543726 0.000000e+00 691.0
11 TraesCS1A01G225800 chr1B 90.385 416 36 4 762 1174 427756972 427757386 5.920000e-151 544.0
12 TraesCS1A01G225800 chr1B 88.732 426 29 7 1654 2077 427523749 427524157 1.000000e-138 503.0
13 TraesCS1A01G225800 chr1B 87.191 445 43 6 1063 1496 427525876 427526317 6.050000e-136 494.0
14 TraesCS1A01G225800 chr1B 86.946 429 55 1 338 766 453522481 453522054 4.710000e-132 481.0
15 TraesCS1A01G225800 chr1B 80.198 707 80 37 938 1604 427774013 427774699 2.190000e-130 475.0
16 TraesCS1A01G225800 chr1B 86.111 432 59 1 332 763 610970941 610971371 4.740000e-127 464.0
17 TraesCS1A01G225800 chr1B 91.150 339 17 9 1 328 427522540 427522876 4.780000e-122 448.0
18 TraesCS1A01G225800 chr1B 90.994 322 17 7 1 314 427750619 427750936 8.050000e-115 424.0
19 TraesCS1A01G225800 chr1B 85.753 372 39 9 2076 2435 384248135 384247766 4.910000e-102 381.0
20 TraesCS1A01G225800 chr6A 87.089 426 54 1 338 763 457075503 457075079 4.710000e-132 481.0
21 TraesCS1A01G225800 chr6A 86.385 426 57 1 338 763 590371407 590370983 4.740000e-127 464.0
22 TraesCS1A01G225800 chr4A 86.343 432 58 1 332 763 69305586 69306016 1.020000e-128 470.0
23 TraesCS1A01G225800 chr4A 83.288 371 36 11 2076 2435 2625263 2625618 3.910000e-83 318.0
24 TraesCS1A01G225800 chr3B 86.620 426 55 2 338 763 12765585 12765162 1.020000e-128 470.0
25 TraesCS1A01G225800 chr3B 86.579 380 32 9 2074 2435 778447485 778447863 3.770000e-108 401.0
26 TraesCS1A01G225800 chr3B 79.019 367 38 18 2073 2435 725857232 725857563 5.270000e-52 215.0
27 TraesCS1A01G225800 chr7A 86.175 434 56 4 332 763 144166707 144167138 1.320000e-127 466.0
28 TraesCS1A01G225800 chr7A 87.003 377 31 11 2072 2435 649980406 649980035 2.250000e-110 409.0
29 TraesCS1A01G225800 chr7A 90.323 62 3 2 2377 2435 139128584 139128645 7.220000e-11 78.7
30 TraesCS1A01G225800 chr4B 86.387 382 31 11 2072 2435 379638437 379638059 4.880000e-107 398.0
31 TraesCS1A01G225800 chr3D 86.022 372 38 10 2074 2435 609903058 609902691 1.060000e-103 387.0
32 TraesCS1A01G225800 chr2A 85.263 380 32 11 2072 2435 10920132 10920503 1.060000e-98 370.0
33 TraesCS1A01G225800 chr2A 90.164 61 3 1 2378 2435 547419987 547420047 2.600000e-10 76.8
34 TraesCS1A01G225800 chr4D 87.888 322 25 7 2076 2393 480297625 480297314 1.380000e-97 366.0
35 TraesCS1A01G225800 chr2B 84.987 373 40 11 2074 2435 653016115 653015748 4.950000e-97 364.0
36 TraesCS1A01G225800 chr2B 86.997 323 31 8 2076 2393 367415538 367415854 1.070000e-93 353.0
37 TraesCS1A01G225800 chr5A 82.940 381 37 11 2074 2435 482617850 482617479 3.910000e-83 318.0
38 TraesCS1A01G225800 chr5A 91.803 61 2 1 2378 2435 709522149 709522089 5.580000e-12 82.4
39 TraesCS1A01G225800 chr5D 93.220 59 3 1 761 819 520681197 520681140 4.310000e-13 86.1


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 TraesCS1A01G225800 chr1A 396261347 396263781 2434 False 4497.00 4497 100.00000 1 2435 1 chr1A.!!$F1 2434
1 TraesCS1A01G225800 chr1A 396283009 396286375 3366 False 554.50 623 81.92800 932 1608 2 chr1A.!!$F3 676
2 TraesCS1A01G225800 chr1D 315615268 315617879 2611 False 1339.50 1923 90.21250 2 2077 2 chr1D.!!$F1 2075
3 TraesCS1A01G225800 chr1D 315640240 315644029 3789 False 572.00 575 82.36550 932 1608 2 chr1D.!!$F2 676
4 TraesCS1A01G225800 chr1B 427771178 427774699 3521 False 762.50 1050 84.12300 938 2077 2 chr1B.!!$F6 1139
5 TraesCS1A01G225800 chr1B 427543028 427543726 698 False 691.00 691 84.99300 914 1604 1 chr1B.!!$F1 690
6 TraesCS1A01G225800 chr1B 427522540 427526317 3777 False 657.75 1186 89.80925 1 2077 4 chr1B.!!$F5 2076

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
392 404 0.036164 GCTGTGTGGTGGTGGTGATA 59.964 55.0 0.0 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 6424 0.035458 CAGCGACTTCTTCACCCCTT 59.965 55.0 0.0 0.0 0.0 3.95 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
279 291 8.469200 ACTAACGTTAGTGTTGGTGCTATATAA 58.531 33.333 34.08 0.00 41.29 0.98
382 394 0.553819 TTTAGTTGGGGCTGTGTGGT 59.446 50.000 0.00 0.00 0.00 4.16
392 404 0.036164 GCTGTGTGGTGGTGGTGATA 59.964 55.000 0.00 0.00 0.00 2.15
394 406 2.632377 CTGTGTGGTGGTGGTGATATC 58.368 52.381 0.00 0.00 0.00 1.63
395 407 1.981495 TGTGTGGTGGTGGTGATATCA 59.019 47.619 0.00 0.00 0.00 2.15
404 416 3.826729 TGGTGGTGATATCACTCGATAGG 59.173 47.826 29.87 0.00 45.73 2.57
416 428 6.576662 TCACTCGATAGGAATAATGTCTCC 57.423 41.667 0.00 0.00 0.00 3.71
423 435 3.104512 AGGAATAATGTCTCCCACGTCA 58.895 45.455 0.00 0.00 31.50 4.35
428 440 3.753294 AATGTCTCCCACGTCATATCC 57.247 47.619 0.00 0.00 0.00 2.59
431 443 1.341531 GTCTCCCACGTCATATCCCTG 59.658 57.143 0.00 0.00 0.00 4.45
436 448 1.338107 CACGTCATATCCCTGCCCTA 58.662 55.000 0.00 0.00 0.00 3.53
458 471 1.138047 GGTGCGAATAGTGTCGTCGG 61.138 60.000 0.00 0.00 43.06 4.79
495 508 1.088340 GTCTCCGTCGGATCTCACGA 61.088 60.000 15.81 4.36 38.32 4.35
496 509 0.392060 TCTCCGTCGGATCTCACGAA 60.392 55.000 15.81 0.00 42.55 3.85
501 514 1.513178 CGTCGGATCTCACGAAATTCG 59.487 52.381 14.35 14.35 46.93 3.34
506 519 1.852895 GATCTCACGAAATTCGGTCGG 59.147 52.381 19.95 6.34 45.59 4.79
517 530 2.430382 TTCGGTCGGTGCTGGTCTTC 62.430 60.000 0.00 0.00 0.00 2.87
547 560 6.658188 TCTATTTGGATCCGGTTTTTGTTT 57.342 33.333 7.39 0.00 0.00 2.83
578 591 3.135225 TCGTGTGGTTACAGGTTTGATG 58.865 45.455 0.00 0.00 41.97 3.07
583 596 4.764823 TGTGGTTACAGGTTTGATGATTCC 59.235 41.667 0.00 0.00 31.91 3.01
593 606 5.817816 AGGTTTGATGATTCCGATCTACAAC 59.182 40.000 0.00 0.00 32.48 3.32
594 607 5.276868 GGTTTGATGATTCCGATCTACAACG 60.277 44.000 0.00 0.00 32.48 4.10
604 617 3.489229 CCGATCTACAACGCTCTTCATCA 60.489 47.826 0.00 0.00 0.00 3.07
606 619 2.881074 TCTACAACGCTCTTCATCAGC 58.119 47.619 0.00 0.00 0.00 4.26
617 630 2.168313 TCTTCATCAGCGATGGTTGCTA 59.832 45.455 15.33 0.00 41.72 3.49
625 638 2.959030 AGCGATGGTTGCTACTCTGATA 59.041 45.455 0.00 0.00 41.87 2.15
628 641 3.677121 CGATGGTTGCTACTCTGATATGC 59.323 47.826 0.00 0.00 0.00 3.14
630 643 5.335976 CGATGGTTGCTACTCTGATATGCTA 60.336 44.000 0.00 0.00 0.00 3.49
653 666 0.679960 ATTTGGGGCCTTAGCACGAC 60.680 55.000 0.84 0.00 46.55 4.34
660 673 1.912371 GCCTTAGCACGACAACTGCC 61.912 60.000 0.00 0.00 39.53 4.85
663 676 2.089887 TTAGCACGACAACTGCCCGA 62.090 55.000 0.00 0.00 35.01 5.14
664 677 2.758770 TAGCACGACAACTGCCCGAC 62.759 60.000 0.00 0.00 35.01 4.79
666 679 1.287815 CACGACAACTGCCCGACTA 59.712 57.895 0.00 0.00 0.00 2.59
693 714 0.744281 CAACAAGGTTTGTCCGGCTT 59.256 50.000 0.00 0.00 44.59 4.35
739 1273 4.116328 CGTCTTCGGCTCGCTCCA 62.116 66.667 0.00 0.00 0.00 3.86
740 1274 2.202676 GTCTTCGGCTCGCTCCAG 60.203 66.667 0.00 0.00 0.00 3.86
751 1285 2.482142 GCTCGCTCCAGTGCTTATAGTT 60.482 50.000 0.00 0.00 0.00 2.24
763 1297 3.446161 TGCTTATAGTTGTCGCTAGGTGT 59.554 43.478 0.00 0.00 0.00 4.16
779 1351 3.149196 AGGTGTTTTCTGTACTGCCATG 58.851 45.455 0.00 0.00 0.00 3.66
781 1353 3.058224 GGTGTTTTCTGTACTGCCATGAC 60.058 47.826 0.00 0.00 0.00 3.06
791 1363 5.604565 TGTACTGCCATGACTGATGAATAG 58.395 41.667 0.00 0.00 33.31 1.73
796 1368 5.067954 TGCCATGACTGATGAATAGATTGG 58.932 41.667 0.00 0.00 33.31 3.16
910 1486 6.980051 AAATAACTTGTGACGACCTATTCC 57.020 37.500 0.00 0.00 0.00 3.01
912 1488 4.345859 AACTTGTGACGACCTATTCCAA 57.654 40.909 0.00 0.00 0.00 3.53
946 2846 0.882927 ACATACACGCAACAACGCCT 60.883 50.000 0.00 0.00 36.19 5.52
1044 2946 5.445142 CCAATCAAGTCTTTCATCTTCGACG 60.445 44.000 0.00 0.00 0.00 5.12
1061 2968 2.240500 CGGCCGAGCTTACAGCATC 61.241 63.158 24.07 0.00 45.56 3.91
1398 3324 1.512734 CAAGCGGTTGATGCGCTTC 60.513 57.895 22.45 15.88 45.53 3.86
1470 3398 0.751643 GTCTGGTTGGTGCTGTGGTT 60.752 55.000 0.00 0.00 0.00 3.67
1528 3468 2.248431 GTTTGTGTGCGCGGAGTC 59.752 61.111 8.83 1.02 0.00 3.36
1571 3514 6.070021 TGGTCCATCTGAACTGAAGTGAATAT 60.070 38.462 0.00 0.00 0.00 1.28
1572 3515 7.125659 TGGTCCATCTGAACTGAAGTGAATATA 59.874 37.037 0.00 0.00 0.00 0.86
1608 3551 4.028383 CGCGCAAAGTGTGAATTATTAGG 58.972 43.478 8.75 0.00 0.00 2.69
1688 3919 0.030638 CTTTCACAAACGGGTGCCAG 59.969 55.000 0.00 0.00 38.66 4.85
1752 3998 8.148999 AGTTACTACAAAGGTTTGGAAGTAGAG 58.851 37.037 14.48 0.00 42.34 2.43
1754 4000 6.522946 ACTACAAAGGTTTGGAAGTAGAGAC 58.477 40.000 7.35 0.00 42.34 3.36
1758 4004 4.009370 AGGTTTGGAAGTAGAGACAAGC 57.991 45.455 0.00 0.00 0.00 4.01
1764 4010 2.354203 GGAAGTAGAGACAAGCCTGGTG 60.354 54.545 0.00 0.00 0.00 4.17
1782 4028 4.883759 TGGTGATGGGAGAGAGAAAGATA 58.116 43.478 0.00 0.00 0.00 1.98
1977 4341 0.455410 GTGTTGCAAGGTGAGCACAA 59.545 50.000 0.00 0.00 42.54 3.33
1991 4355 1.506262 CACAACGGGCCTTATGCAC 59.494 57.895 0.84 0.00 43.89 4.57
2021 4386 6.795098 AAACAAAAGGGTTTGACTTGTTTC 57.205 33.333 6.21 0.00 45.99 2.78
2031 4396 1.134220 TGACTTGTTTCGGCTTGTCCT 60.134 47.619 0.00 0.00 0.00 3.85
2069 4434 4.160252 GGAACTCCATGCAACCAAATGTAT 59.840 41.667 0.00 0.00 35.64 2.29
2077 4442 5.186256 TGCAACCAAATGTATCCCTAAGA 57.814 39.130 0.00 0.00 0.00 2.10
2078 4443 5.192927 TGCAACCAAATGTATCCCTAAGAG 58.807 41.667 0.00 0.00 0.00 2.85
2079 4444 4.036852 GCAACCAAATGTATCCCTAAGAGC 59.963 45.833 0.00 0.00 0.00 4.09
2080 4445 5.192927 CAACCAAATGTATCCCTAAGAGCA 58.807 41.667 0.00 0.00 0.00 4.26
2082 4447 5.625150 ACCAAATGTATCCCTAAGAGCATC 58.375 41.667 0.00 0.00 0.00 3.91
2093 4458 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
2118 4483 2.512974 AGGGGGCGCGTAAAATCG 60.513 61.111 8.43 0.00 0.00 3.34
2126 4491 3.788817 CGTAAAATCGCCGCCTGA 58.211 55.556 0.00 0.00 0.00 3.86
2127 4492 1.636340 CGTAAAATCGCCGCCTGAG 59.364 57.895 0.00 0.00 0.00 3.35
2150 4515 2.895372 AGCCGGCGCTAAAATCGG 60.895 61.111 23.20 15.00 46.08 4.18
2156 4521 2.707039 CGCTAAAATCGGCGTGGG 59.293 61.111 6.85 0.00 45.34 4.61
2159 4524 2.438795 TAAAATCGGCGTGGGGGC 60.439 61.111 6.85 0.00 37.98 5.80
2209 4574 2.587889 CCCCCAGACGCCGTATTT 59.412 61.111 0.00 0.00 0.00 1.40
2240 5242 7.190920 AGAAAAGGTATTCGACAAAGTTCAG 57.809 36.000 0.00 0.00 34.46 3.02
2241 5243 5.358298 AAAGGTATTCGACAAAGTTCAGC 57.642 39.130 0.00 0.00 0.00 4.26
2245 5247 5.473504 AGGTATTCGACAAAGTTCAGCAAAT 59.526 36.000 0.00 0.00 0.00 2.32
2247 5249 6.640907 GGTATTCGACAAAGTTCAGCAAATTT 59.359 34.615 0.00 0.00 29.85 1.82
2250 5252 5.034152 TCGACAAAGTTCAGCAAATTTGAC 58.966 37.500 22.31 12.64 46.09 3.18
2251 5253 5.301500 GACAAAGTTCAGCAAATTTGACG 57.699 39.130 22.31 11.20 46.09 4.35
2254 5256 5.516339 ACAAAGTTCAGCAAATTTGACGAAG 59.484 36.000 22.31 12.07 46.09 3.79
2272 5274 6.009115 ACGAAGTATTTGGCTAAAGTTTGG 57.991 37.500 0.65 0.00 41.94 3.28
2273 5275 5.766174 ACGAAGTATTTGGCTAAAGTTTGGA 59.234 36.000 2.72 0.00 41.94 3.53
2274 5276 6.263617 ACGAAGTATTTGGCTAAAGTTTGGAA 59.736 34.615 2.72 0.00 41.94 3.53
2275 5277 7.142680 CGAAGTATTTGGCTAAAGTTTGGAAA 58.857 34.615 2.72 0.00 0.00 3.13
2276 5278 7.650104 CGAAGTATTTGGCTAAAGTTTGGAAAA 59.350 33.333 2.72 3.36 0.00 2.29
2277 5279 8.657074 AAGTATTTGGCTAAAGTTTGGAAAAC 57.343 30.769 2.72 0.00 0.00 2.43
2279 5281 9.138596 AGTATTTGGCTAAAGTTTGGAAAACTA 57.861 29.630 2.72 0.00 0.00 2.24
2280 5282 9.406828 GTATTTGGCTAAAGTTTGGAAAACTAG 57.593 33.333 2.72 2.77 0.00 2.57
2281 5283 7.648039 TTTGGCTAAAGTTTGGAAAACTAGA 57.352 32.000 2.72 0.00 0.00 2.43
2282 5284 6.628919 TGGCTAAAGTTTGGAAAACTAGAC 57.371 37.500 2.72 4.13 0.00 2.59
2283 5285 6.123651 TGGCTAAAGTTTGGAAAACTAGACA 58.876 36.000 2.72 6.48 0.00 3.41
2284 5286 6.775629 TGGCTAAAGTTTGGAAAACTAGACAT 59.224 34.615 2.72 0.00 0.00 3.06
2285 5287 7.940137 TGGCTAAAGTTTGGAAAACTAGACATA 59.060 33.333 2.72 0.00 0.00 2.29
2286 5288 8.957466 GGCTAAAGTTTGGAAAACTAGACATAT 58.043 33.333 2.72 0.00 0.00 1.78
2348 6426 5.813080 AAAAGGCCGCAACTATAACTAAG 57.187 39.130 0.00 0.00 0.00 2.18
2349 6427 3.470645 AGGCCGCAACTATAACTAAGG 57.529 47.619 0.00 0.00 0.00 2.69
2350 6428 2.104281 AGGCCGCAACTATAACTAAGGG 59.896 50.000 0.00 0.00 0.00 3.95
2351 6429 2.490991 GCCGCAACTATAACTAAGGGG 58.509 52.381 0.00 0.00 0.00 4.79
2352 6430 2.158856 GCCGCAACTATAACTAAGGGGT 60.159 50.000 0.00 0.00 0.00 4.95
2353 6431 3.463944 CCGCAACTATAACTAAGGGGTG 58.536 50.000 0.00 0.00 0.00 4.61
2354 6432 3.133362 CCGCAACTATAACTAAGGGGTGA 59.867 47.826 0.00 0.00 0.00 4.02
2355 6433 4.383335 CCGCAACTATAACTAAGGGGTGAA 60.383 45.833 0.00 0.00 0.00 3.18
2357 6435 5.394883 CGCAACTATAACTAAGGGGTGAAGA 60.395 44.000 0.00 0.00 0.00 2.87
2358 6436 6.412214 GCAACTATAACTAAGGGGTGAAGAA 58.588 40.000 0.00 0.00 0.00 2.52
2359 6437 6.539103 GCAACTATAACTAAGGGGTGAAGAAG 59.461 42.308 0.00 0.00 0.00 2.85
2360 6438 7.621796 CAACTATAACTAAGGGGTGAAGAAGT 58.378 38.462 0.00 0.00 0.00 3.01
2361 6439 7.421087 ACTATAACTAAGGGGTGAAGAAGTC 57.579 40.000 0.00 0.00 0.00 3.01
2362 6440 3.679824 AACTAAGGGGTGAAGAAGTCG 57.320 47.619 0.00 0.00 0.00 4.18
2365 6443 0.035458 AAGGGGTGAAGAAGTCGCTG 59.965 55.000 0.00 0.00 36.92 5.18
2367 6445 0.390472 GGGGTGAAGAAGTCGCTGAG 60.390 60.000 0.00 0.00 36.92 3.35
2368 6446 1.016653 GGGTGAAGAAGTCGCTGAGC 61.017 60.000 0.00 0.00 36.92 4.26
2418 7046 3.403558 GGCGGCCTTCTCCTCCTT 61.404 66.667 12.87 0.00 0.00 3.36
2419 7047 2.124942 GCGGCCTTCTCCTCCTTG 60.125 66.667 0.00 0.00 0.00 3.61
2421 7049 1.219393 CGGCCTTCTCCTCCTTGAC 59.781 63.158 0.00 0.00 0.00 3.18
2422 7050 1.219393 GGCCTTCTCCTCCTTGACG 59.781 63.158 0.00 0.00 0.00 4.35
2423 7051 1.448717 GCCTTCTCCTCCTTGACGC 60.449 63.158 0.00 0.00 0.00 5.19
2424 7052 1.153745 CCTTCTCCTCCTTGACGCG 60.154 63.158 3.53 3.53 0.00 6.01
2427 7055 1.874345 TTCTCCTCCTTGACGCGGAC 61.874 60.000 12.47 4.63 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.869342 CGGCATGTGCATCGAGTCATA 60.869 52.381 7.36 0.00 44.36 2.15
279 291 5.458595 AGTTGACTTTCCTTCCCTTTTGAT 58.541 37.500 0.00 0.00 0.00 2.57
328 340 9.425577 CCTAACAAAAACAAAAACAAGGTCTTA 57.574 29.630 0.00 0.00 0.00 2.10
353 365 5.221561 ACAGCCCCAACTAAAACATTAAACC 60.222 40.000 0.00 0.00 0.00 3.27
363 375 0.553819 ACCACACAGCCCCAACTAAA 59.446 50.000 0.00 0.00 0.00 1.85
367 379 2.912025 CCACCACACAGCCCCAAC 60.912 66.667 0.00 0.00 0.00 3.77
371 383 4.204028 ACCACCACCACACAGCCC 62.204 66.667 0.00 0.00 0.00 5.19
392 404 6.153680 GGGAGACATTATTCCTATCGAGTGAT 59.846 42.308 0.00 0.00 38.67 3.06
394 406 5.243954 TGGGAGACATTATTCCTATCGAGTG 59.756 44.000 0.00 0.00 33.85 3.51
395 407 5.244178 GTGGGAGACATTATTCCTATCGAGT 59.756 44.000 0.00 0.00 33.85 4.18
404 416 5.869888 GGATATGACGTGGGAGACATTATTC 59.130 44.000 0.00 0.00 0.00 1.75
416 428 1.071471 GGGCAGGGATATGACGTGG 59.929 63.158 0.00 0.00 0.00 4.94
423 435 1.355720 GCACCATTAGGGCAGGGATAT 59.644 52.381 0.00 0.00 42.05 1.63
428 440 0.466189 ATTCGCACCATTAGGGCAGG 60.466 55.000 0.00 0.00 42.05 4.85
431 443 1.873591 CACTATTCGCACCATTAGGGC 59.126 52.381 0.00 0.00 42.05 5.19
436 448 2.268298 GACGACACTATTCGCACCATT 58.732 47.619 0.00 0.00 43.06 3.16
458 471 4.180057 GAGACACATCTCCACACATTCTC 58.820 47.826 0.00 0.00 45.06 2.87
495 508 0.953960 GACCAGCACCGACCGAATTT 60.954 55.000 0.00 0.00 0.00 1.82
496 509 1.375523 GACCAGCACCGACCGAATT 60.376 57.895 0.00 0.00 0.00 2.17
501 514 2.432628 CGAAGACCAGCACCGACC 60.433 66.667 0.00 0.00 0.00 4.79
506 519 0.741221 GATCCACCGAAGACCAGCAC 60.741 60.000 0.00 0.00 0.00 4.40
537 550 4.618067 ACGAACGAAAGACAAACAAAAACC 59.382 37.500 0.14 0.00 0.00 3.27
547 560 2.012937 AACCACACGAACGAAAGACA 57.987 45.000 0.14 0.00 0.00 3.41
578 591 3.357166 AGAGCGTTGTAGATCGGAATC 57.643 47.619 0.00 0.00 0.00 2.52
583 596 3.695816 TGATGAAGAGCGTTGTAGATCG 58.304 45.455 0.00 0.00 0.00 3.69
594 607 1.329906 CAACCATCGCTGATGAAGAGC 59.670 52.381 16.69 0.00 42.09 4.09
604 617 1.186200 TCAGAGTAGCAACCATCGCT 58.814 50.000 0.00 0.00 43.62 4.93
606 619 3.677121 GCATATCAGAGTAGCAACCATCG 59.323 47.826 0.00 0.00 0.00 3.84
617 630 5.221803 CCCCAAATGACTAGCATATCAGAGT 60.222 44.000 0.00 0.00 35.78 3.24
625 638 0.929244 AGGCCCCAAATGACTAGCAT 59.071 50.000 0.00 0.00 39.43 3.79
628 641 2.092429 TGCTAAGGCCCCAAATGACTAG 60.092 50.000 0.00 0.00 37.74 2.57
630 643 0.704076 TGCTAAGGCCCCAAATGACT 59.296 50.000 0.00 0.00 37.74 3.41
653 666 3.630769 TGTAGTAGATAGTCGGGCAGTTG 59.369 47.826 0.00 0.00 0.00 3.16
660 673 5.831702 ACCTTGTTGTAGTAGATAGTCGG 57.168 43.478 0.00 0.00 0.00 4.79
663 676 7.384477 GGACAAACCTTGTTGTAGTAGATAGT 58.616 38.462 0.00 0.00 45.52 2.12
664 677 6.530534 CGGACAAACCTTGTTGTAGTAGATAG 59.469 42.308 0.00 0.00 45.52 2.08
666 679 5.235516 CGGACAAACCTTGTTGTAGTAGAT 58.764 41.667 0.00 0.00 45.52 1.98
697 718 2.764128 GTCATCGCCCCTCCCTCA 60.764 66.667 0.00 0.00 0.00 3.86
699 720 2.765807 CTGTCATCGCCCCTCCCT 60.766 66.667 0.00 0.00 0.00 4.20
721 1255 4.117661 GGAGCGAGCCGAAGACGT 62.118 66.667 0.00 0.00 37.88 4.34
724 1258 2.676822 ACTGGAGCGAGCCGAAGA 60.677 61.111 0.00 0.00 0.00 2.87
739 1273 3.700038 ACCTAGCGACAACTATAAGCACT 59.300 43.478 0.00 0.00 0.00 4.40
740 1274 3.797256 CACCTAGCGACAACTATAAGCAC 59.203 47.826 0.00 0.00 0.00 4.40
751 1285 2.902705 ACAGAAAACACCTAGCGACA 57.097 45.000 0.00 0.00 0.00 4.35
763 1297 4.350368 TCAGTCATGGCAGTACAGAAAA 57.650 40.909 0.00 0.00 0.00 2.29
815 1389 3.577848 TGTGCTGGAATATGGTTGCTTTT 59.422 39.130 0.00 0.00 0.00 2.27
910 1486 6.354858 GTGTATGTACACGATGCATATGTTG 58.645 40.000 18.44 7.81 45.87 3.33
946 2846 1.332375 GCGTGCTAGTGTGTTGGAAAA 59.668 47.619 0.00 0.00 0.00 2.29
1061 2968 0.445436 GCTGCAAGACATCCTTCGTG 59.555 55.000 0.00 0.00 34.07 4.35
1398 3324 1.165907 ACACACGGCACAATCACCAG 61.166 55.000 0.00 0.00 0.00 4.00
1463 3391 3.069443 ACCAATAGCAAACCAAACCACAG 59.931 43.478 0.00 0.00 0.00 3.66
1470 3398 4.404073 ACAAAGACACCAATAGCAAACCAA 59.596 37.500 0.00 0.00 0.00 3.67
1528 3468 5.473162 TGGACCATTTCAAAGACACACATAG 59.527 40.000 0.00 0.00 0.00 2.23
1571 3514 2.414806 TGCGCGAACCTGTTTTGTATA 58.585 42.857 12.10 0.00 0.00 1.47
1572 3515 1.231221 TGCGCGAACCTGTTTTGTAT 58.769 45.000 12.10 0.00 0.00 2.29
1608 3551 9.654663 AATAAGATAGAAATATGTAAGACGCCC 57.345 33.333 0.00 0.00 0.00 6.13
1677 3908 3.454812 AGAGAAATATACTGGCACCCGTT 59.545 43.478 0.00 0.00 0.00 4.44
1727 3958 8.146412 TCTCTACTTCCAAACCTTTGTAGTAAC 58.854 37.037 0.00 0.00 35.20 2.50
1744 3990 2.563179 TCACCAGGCTTGTCTCTACTTC 59.437 50.000 0.00 0.00 0.00 3.01
1752 3998 0.393537 CTCCCATCACCAGGCTTGTC 60.394 60.000 0.00 0.00 0.00 3.18
1754 4000 0.107312 CTCTCCCATCACCAGGCTTG 60.107 60.000 0.00 0.00 0.00 4.01
1758 4004 1.871418 TTCTCTCTCCCATCACCAGG 58.129 55.000 0.00 0.00 0.00 4.45
1764 4010 8.567285 TTGTTTTTATCTTTCTCTCTCCCATC 57.433 34.615 0.00 0.00 0.00 3.51
1782 4028 8.585018 AGCCTACTTAATGCATAACTTGTTTTT 58.415 29.630 0.00 0.00 0.00 1.94
1796 4042 7.865706 ACACAATCCTTAAGCCTACTTAATG 57.134 36.000 0.00 0.00 45.12 1.90
1935 4299 2.081462 GTGGTGAAATTACCCACTCGG 58.919 52.381 11.79 0.00 44.21 4.63
1977 4341 3.910914 TTGCGTGCATAAGGCCCGT 62.911 57.895 0.00 0.00 45.62 5.28
1991 4355 2.017138 AACCCTTTTGTTTGGTTGCG 57.983 45.000 0.00 0.00 40.75 4.85
2016 4381 0.468226 ACTGAGGACAAGCCGAAACA 59.532 50.000 0.00 0.00 43.43 2.83
2021 4386 0.535102 AAACCACTGAGGACAAGCCG 60.535 55.000 0.00 0.00 43.43 5.52
2031 4396 1.283613 AGTTCCCACACAAACCACTGA 59.716 47.619 0.00 0.00 0.00 3.41
2069 4434 1.418334 GCTGGAGATGCTCTTAGGGA 58.582 55.000 0.00 0.00 0.00 4.20
2100 4465 2.819552 CGATTTTACGCGCCCCCTG 61.820 63.158 5.73 0.00 0.00 4.45
2101 4466 2.512974 CGATTTTACGCGCCCCCT 60.513 61.111 5.73 0.00 0.00 4.79
2110 4475 1.436983 CCCTCAGGCGGCGATTTTAC 61.437 60.000 12.98 0.00 0.00 2.01
2113 4478 4.489771 CCCCTCAGGCGGCGATTT 62.490 66.667 12.98 0.00 0.00 2.17
2135 4500 4.293626 CGCCGATTTTAGCGCCGG 62.294 66.667 15.00 15.00 46.50 6.13
2140 4505 2.478033 CCCCCACGCCGATTTTAGC 61.478 63.158 0.00 0.00 0.00 3.09
2141 4506 2.478033 GCCCCCACGCCGATTTTAG 61.478 63.158 0.00 0.00 0.00 1.85
2142 4507 2.438795 GCCCCCACGCCGATTTTA 60.439 61.111 0.00 0.00 0.00 1.52
2191 4556 3.692370 AAATACGGCGTCTGGGGGC 62.692 63.158 19.21 0.00 0.00 5.80
2214 4579 7.992008 TGAACTTTGTCGAATACCTTTTCTTT 58.008 30.769 0.00 0.00 0.00 2.52
2215 4580 7.562454 TGAACTTTGTCGAATACCTTTTCTT 57.438 32.000 0.00 0.00 0.00 2.52
2219 4584 4.819630 TGCTGAACTTTGTCGAATACCTTT 59.180 37.500 0.00 0.00 0.00 3.11
2220 4585 4.385825 TGCTGAACTTTGTCGAATACCTT 58.614 39.130 0.00 0.00 0.00 3.50
2221 4586 4.002906 TGCTGAACTTTGTCGAATACCT 57.997 40.909 0.00 0.00 0.00 3.08
2223 4588 7.378461 TCAAATTTGCTGAACTTTGTCGAATAC 59.622 33.333 13.54 0.00 31.98 1.89
2224 4589 7.378461 GTCAAATTTGCTGAACTTTGTCGAATA 59.622 33.333 13.54 0.00 31.98 1.75
2227 4592 5.034152 GTCAAATTTGCTGAACTTTGTCGA 58.966 37.500 13.54 0.00 31.98 4.20
2231 4596 5.516339 ACTTCGTCAAATTTGCTGAACTTTG 59.484 36.000 13.54 9.50 0.00 2.77
2235 5237 7.358352 CCAAATACTTCGTCAAATTTGCTGAAC 60.358 37.037 13.54 5.57 37.78 3.18
2240 5242 4.923281 AGCCAAATACTTCGTCAAATTTGC 59.077 37.500 13.54 7.78 37.78 3.68
2241 5243 8.514136 TTTAGCCAAATACTTCGTCAAATTTG 57.486 30.769 12.15 12.15 38.47 2.32
2245 5247 6.870971 ACTTTAGCCAAATACTTCGTCAAA 57.129 33.333 0.00 0.00 0.00 2.69
2247 5249 6.293735 CCAAACTTTAGCCAAATACTTCGTCA 60.294 38.462 0.00 0.00 0.00 4.35
2248 5250 6.072893 TCCAAACTTTAGCCAAATACTTCGTC 60.073 38.462 0.00 0.00 0.00 4.20
2250 5252 6.249035 TCCAAACTTTAGCCAAATACTTCG 57.751 37.500 0.00 0.00 0.00 3.79
2251 5253 8.761497 GTTTTCCAAACTTTAGCCAAATACTTC 58.239 33.333 0.00 0.00 0.00 3.01
2254 5256 9.406828 CTAGTTTTCCAAACTTTAGCCAAATAC 57.593 33.333 7.17 0.00 0.00 1.89
2325 5327 5.124936 CCTTAGTTATAGTTGCGGCCTTTTT 59.875 40.000 0.00 0.00 0.00 1.94
2326 5328 4.638865 CCTTAGTTATAGTTGCGGCCTTTT 59.361 41.667 0.00 0.00 0.00 2.27
2327 5329 4.196971 CCTTAGTTATAGTTGCGGCCTTT 58.803 43.478 0.00 0.00 0.00 3.11
2328 5330 3.433173 CCCTTAGTTATAGTTGCGGCCTT 60.433 47.826 0.00 0.00 0.00 4.35
2329 5331 2.104281 CCCTTAGTTATAGTTGCGGCCT 59.896 50.000 0.00 0.00 0.00 5.19
2333 5335 4.395959 TCACCCCTTAGTTATAGTTGCG 57.604 45.455 0.00 0.00 0.00 4.85
2345 6423 1.275291 CAGCGACTTCTTCACCCCTTA 59.725 52.381 0.00 0.00 0.00 2.69
2346 6424 0.035458 CAGCGACTTCTTCACCCCTT 59.965 55.000 0.00 0.00 0.00 3.95
2347 6425 0.832135 TCAGCGACTTCTTCACCCCT 60.832 55.000 0.00 0.00 0.00 4.79
2348 6426 0.390472 CTCAGCGACTTCTTCACCCC 60.390 60.000 0.00 0.00 0.00 4.95
2349 6427 1.016653 GCTCAGCGACTTCTTCACCC 61.017 60.000 0.00 0.00 0.00 4.61
2350 6428 2.450619 GCTCAGCGACTTCTTCACC 58.549 57.895 0.00 0.00 0.00 4.02
2402 7030 2.124942 CAAGGAGGAGAAGGCCGC 60.125 66.667 0.00 0.00 0.00 6.53
2406 7034 1.153745 CGCGTCAAGGAGGAGAAGG 60.154 63.158 0.00 0.00 0.00 3.46
2408 7036 1.605451 TCCGCGTCAAGGAGGAGAA 60.605 57.895 4.92 0.00 31.84 2.87
2409 7037 2.035155 TCCGCGTCAAGGAGGAGA 59.965 61.111 4.92 0.00 31.84 3.71
2410 7038 2.182030 GTCCGCGTCAAGGAGGAG 59.818 66.667 4.92 0.00 38.65 3.69


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

AutoCloner maintained by Alex Coulton.