Multiple sequence alignment - TraesCS1A01G298800

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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 TraesCS1A01G298800 chr1A 100.000 2862 0 0 1 2862 493735815 493738676 0.000000e+00 5286
1 TraesCS1A01G298800 chr1D 91.038 1763 95 26 423 2156 391340895 391339167 0.000000e+00 2322
2 TraesCS1A01G298800 chr1D 88.967 426 39 3 4 421 391445381 391444956 1.180000e-143 520
3 TraesCS1A01G298800 chr1D 89.250 400 25 6 2312 2699 391334863 391334470 4.290000e-133 484
4 TraesCS1A01G298800 chr1D 91.623 191 9 1 2672 2862 391331519 391331336 1.020000e-64 257
5 TraesCS1A01G298800 chr1D 100.000 40 0 0 2154 2193 391339117 391339078 1.100000e-09 75
6 TraesCS1A01G298800 chr1B 90.091 1544 84 25 600 2112 531165644 531167149 0.000000e+00 1940
7 TraesCS1A01G298800 chr1B 89.902 614 47 6 1 602 531151954 531152564 0.000000e+00 776
8 TraesCS1A01G298800 chr1B 83.920 653 82 19 2226 2862 531168258 531168903 1.130000e-168 603
9 TraesCS1A01G298800 chr6D 78.547 289 55 6 2573 2857 342439259 342438974 1.750000e-42 183


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 TraesCS1A01G298800 chr1A 493735815 493738676 2861 False 5286.0 5286 100.0000 1 2862 1 chr1A.!!$F1 2861
1 TraesCS1A01G298800 chr1D 391339078 391340895 1817 True 1198.5 2322 95.5190 423 2193 2 chr1D.!!$R3 1770
2 TraesCS1A01G298800 chr1D 391331336 391334863 3527 True 370.5 484 90.4365 2312 2862 2 chr1D.!!$R2 550
3 TraesCS1A01G298800 chr1B 531165644 531168903 3259 False 1271.5 1940 87.0055 600 2862 2 chr1B.!!$F2 2262
4 TraesCS1A01G298800 chr1B 531151954 531152564 610 False 776.0 776 89.9020 1 602 1 chr1B.!!$F1 601

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
490 502 0.319900 CTTCTCGACCCACCTGTGTG 60.320 60.0 0.0 0.0 42.39 3.82 F
1207 1237 0.324091 GGAGAAGGAGGTACGGGACA 60.324 60.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1491 0.034960 GAAGGAGGAAGACAAGGCCC 60.035 60.0 0.0 0.0 0.00 5.80 R
2207 3232 0.692476 ACTACTGCCATGCACCTTCA 59.308 50.0 0.0 0.0 33.79 3.02 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
51 52 2.288152 CGCCTCTGCTTCCTCTCTAATC 60.288 54.545 0.00 0.00 34.43 1.75
53 54 3.387699 GCCTCTGCTTCCTCTCTAATCTT 59.612 47.826 0.00 0.00 33.53 2.40
84 85 5.984695 TCTCCATAGCATATACACACTCC 57.015 43.478 0.00 0.00 0.00 3.85
118 119 1.869767 CCCTAGAATCAGCATTGTCGC 59.130 52.381 0.00 0.00 0.00 5.19
126 127 2.832931 AGCATTGTCGCTGACTCAC 58.167 52.632 9.49 0.00 41.85 3.51
133 134 1.753078 TCGCTGACTCACGGGCTAT 60.753 57.895 0.00 0.00 0.00 2.97
136 137 1.360551 CTGACTCACGGGCTATCGG 59.639 63.158 0.00 0.00 0.00 4.18
150 151 1.955080 CTATCGGAGTAGACACCACCC 59.045 57.143 0.00 0.00 0.00 4.61
164 165 1.203570 ACCACCCCCATAGAGAAACCT 60.204 52.381 0.00 0.00 0.00 3.50
171 172 2.158957 CCCATAGAGAAACCTTAGCGCA 60.159 50.000 11.47 0.00 0.00 6.09
176 177 6.404734 CCATAGAGAAACCTTAGCGCAAATTT 60.405 38.462 11.47 2.20 0.00 1.82
199 200 0.467384 CTCATGATCGCCTTCCCTGT 59.533 55.000 0.00 0.00 0.00 4.00
225 226 2.645192 GGGTTTTCCGCATGGTGGG 61.645 63.158 0.00 0.00 41.82 4.61
262 263 5.515184 GGCTAGTAGCTAGGATCTCCAAGTA 60.515 48.000 21.20 0.00 41.99 2.24
297 308 2.734079 CGTGCATGTATGTGTGTGTGTA 59.266 45.455 0.00 0.00 0.00 2.90
333 344 3.193267 TCATGGCAAGTGGTATTTGAAGC 59.807 43.478 0.00 0.00 0.00 3.86
357 369 3.402628 TTGCTTAGAGTGGTTCACCTC 57.597 47.619 0.00 0.00 34.49 3.85
368 380 2.636412 TTCACCTCTGGGACTCGCG 61.636 63.158 0.00 0.00 36.25 5.87
377 389 2.258726 GGGACTCGCGCAGGTTTTT 61.259 57.895 8.75 0.00 0.00 1.94
385 397 4.541020 GCAGGTTTTTGCGCTCTC 57.459 55.556 9.73 0.00 33.90 3.20
386 398 1.081175 GCAGGTTTTTGCGCTCTCC 60.081 57.895 9.73 4.26 33.90 3.71
391 403 1.327764 GGTTTTTGCGCTCTCCGATAG 59.672 52.381 9.73 0.00 40.02 2.08
405 417 3.454375 TCCGATAGCGTCAATTCTTTCC 58.546 45.455 0.00 0.00 35.23 3.13
421 433 3.517901 TCTTTCCGAGATTGAAGGGCTAA 59.482 43.478 0.00 0.00 0.00 3.09
443 455 4.377897 ACCTCGTCGTTTCATTCTTTCTT 58.622 39.130 0.00 0.00 0.00 2.52
484 496 2.249844 TTTCAACTTCTCGACCCACC 57.750 50.000 0.00 0.00 0.00 4.61
489 501 0.759436 ACTTCTCGACCCACCTGTGT 60.759 55.000 0.00 0.00 0.00 3.72
490 502 0.319900 CTTCTCGACCCACCTGTGTG 60.320 60.000 0.00 0.00 42.39 3.82
497 509 0.324275 ACCCACCTGTGTGCAAAACT 60.324 50.000 0.00 0.00 41.35 2.66
498 510 0.823460 CCCACCTGTGTGCAAAACTT 59.177 50.000 0.00 0.00 41.35 2.66
509 521 2.287059 CAAAACTTGCACGCACACC 58.713 52.632 0.00 0.00 0.00 4.16
533 545 1.375908 TGACGAGTTGCTGGATGGC 60.376 57.895 0.00 0.00 0.00 4.40
550 563 3.415087 CCTCCCCCTGGCTTCCTG 61.415 72.222 0.00 0.00 0.00 3.86
569 582 1.135139 TGACGACTAGCTTGATGGCTC 59.865 52.381 1.04 0.00 42.97 4.70
581 599 1.701292 TGATGGCTCATCATGTAGGGG 59.299 52.381 12.22 0.00 44.60 4.79
590 608 0.846015 TCATGTAGGGGGCCATTGAG 59.154 55.000 4.39 0.00 0.00 3.02
610 628 9.153721 CATTGAGGCTTGAATAAATTAAAAGCA 57.846 29.630 17.60 4.86 39.46 3.91
611 629 9.895138 ATTGAGGCTTGAATAAATTAAAAGCAT 57.105 25.926 17.60 13.43 39.46 3.79
627 645 6.544038 AAAAGCATTTAATTTCCTGCACAC 57.456 33.333 8.07 0.00 37.28 3.82
726 755 4.505918 CCAGTGTCCACCAAATTACCTACA 60.506 45.833 0.00 0.00 0.00 2.74
728 757 4.595781 AGTGTCCACCAAATTACCTACAGA 59.404 41.667 0.00 0.00 0.00 3.41
787 817 1.901948 AGGAGAACGTGGCGACTGA 60.902 57.895 0.00 0.00 0.00 3.41
788 818 1.733399 GGAGAACGTGGCGACTGAC 60.733 63.158 0.00 0.00 0.00 3.51
935 965 2.006888 CACTCGTTTTCTGGTGTGTGT 58.993 47.619 0.00 0.00 0.00 3.72
936 966 2.006888 ACTCGTTTTCTGGTGTGTGTG 58.993 47.619 0.00 0.00 0.00 3.82
937 967 2.006888 CTCGTTTTCTGGTGTGTGTGT 58.993 47.619 0.00 0.00 0.00 3.72
938 968 1.735018 TCGTTTTCTGGTGTGTGTGTG 59.265 47.619 0.00 0.00 0.00 3.82
939 969 1.466950 CGTTTTCTGGTGTGTGTGTGT 59.533 47.619 0.00 0.00 0.00 3.72
940 970 2.727607 CGTTTTCTGGTGTGTGTGTGTG 60.728 50.000 0.00 0.00 0.00 3.82
941 971 2.192664 TTTCTGGTGTGTGTGTGTGT 57.807 45.000 0.00 0.00 0.00 3.72
942 972 1.447945 TTCTGGTGTGTGTGTGTGTG 58.552 50.000 0.00 0.00 0.00 3.82
1029 1059 0.822532 CTGCCCAATCCATGCTCTCC 60.823 60.000 0.00 0.00 0.00 3.71
1103 1133 2.367512 AGGAGGAGGGGGCATCAC 60.368 66.667 0.00 0.00 0.00 3.06
1125 1155 1.569493 CGGCAACAGGTTCTTGACG 59.431 57.895 0.00 0.00 43.36 4.35
1207 1237 0.324091 GGAGAAGGAGGTACGGGACA 60.324 60.000 0.00 0.00 0.00 4.02
1228 1258 6.307031 ACATATCTAGCTACTCGTGTCTTG 57.693 41.667 0.00 0.00 0.00 3.02
1229 1259 3.701532 ATCTAGCTACTCGTGTCTTGC 57.298 47.619 0.00 0.00 0.00 4.01
1238 1271 0.376852 TCGTGTCTTGCTGTTGTTGC 59.623 50.000 0.00 0.00 0.00 4.17
1263 1296 3.999001 CTGCTGCTGTTATCTGAACTTGA 59.001 43.478 0.00 0.00 0.00 3.02
1270 1303 6.038603 TGCTGTTATCTGAACTTGAATATGCC 59.961 38.462 0.00 0.00 0.00 4.40
1271 1304 6.261826 GCTGTTATCTGAACTTGAATATGCCT 59.738 38.462 0.00 0.00 0.00 4.75
1272 1305 7.558161 TGTTATCTGAACTTGAATATGCCTG 57.442 36.000 0.00 0.00 0.00 4.85
1431 1464 3.690745 AGGTACGCGCAACCTACT 58.309 55.556 27.12 8.51 45.69 2.57
1432 1465 1.509923 AGGTACGCGCAACCTACTC 59.490 57.895 27.12 7.76 45.69 2.59
1435 1468 0.734889 GTACGCGCAACCTACTCCTA 59.265 55.000 5.73 0.00 0.00 2.94
1441 1474 2.652590 CGCAACCTACTCCTACTACCT 58.347 52.381 0.00 0.00 0.00 3.08
1446 1479 5.243507 GCAACCTACTCCTACTACCTATTCC 59.756 48.000 0.00 0.00 0.00 3.01
1447 1480 6.371278 CAACCTACTCCTACTACCTATTCCA 58.629 44.000 0.00 0.00 0.00 3.53
1449 1482 7.176909 ACCTACTCCTACTACCTATTCCATT 57.823 40.000 0.00 0.00 0.00 3.16
1450 1483 7.240167 ACCTACTCCTACTACCTATTCCATTC 58.760 42.308 0.00 0.00 0.00 2.67
1451 1484 7.075267 ACCTACTCCTACTACCTATTCCATTCT 59.925 40.741 0.00 0.00 0.00 2.40
1452 1485 7.951245 CCTACTCCTACTACCTATTCCATTCTT 59.049 40.741 0.00 0.00 0.00 2.52
1453 1486 7.604657 ACTCCTACTACCTATTCCATTCTTG 57.395 40.000 0.00 0.00 0.00 3.02
1454 1487 7.133483 ACTCCTACTACCTATTCCATTCTTGT 58.867 38.462 0.00 0.00 0.00 3.16
1455 1488 7.288158 ACTCCTACTACCTATTCCATTCTTGTC 59.712 40.741 0.00 0.00 0.00 3.18
1456 1489 7.130099 TCCTACTACCTATTCCATTCTTGTCA 58.870 38.462 0.00 0.00 0.00 3.58
1457 1490 7.622081 TCCTACTACCTATTCCATTCTTGTCAA 59.378 37.037 0.00 0.00 0.00 3.18
1458 1491 7.928706 CCTACTACCTATTCCATTCTTGTCAAG 59.071 40.741 6.21 6.21 0.00 3.02
1473 1513 0.693049 TCAAGGGCCTTGTCTTCCTC 59.307 55.000 37.83 0.00 41.66 3.71
1486 1526 0.105778 CTTCCTCCTTCTCGGCATCC 59.894 60.000 0.00 0.00 0.00 3.51
1490 1530 0.471617 CTCCTTCTCGGCATCCCAAT 59.528 55.000 0.00 0.00 0.00 3.16
1825 1876 1.840635 GATTCACCCACCTTAGAGGCT 59.159 52.381 0.00 0.00 39.63 4.58
1829 1880 0.984995 ACCCACCTTAGAGGCTGAAC 59.015 55.000 0.00 0.00 39.63 3.18
1871 1922 1.775770 CGTCGTCGTGAGCTGATAATG 59.224 52.381 0.00 0.00 0.00 1.90
1925 1976 5.879237 TCGAAGCATAAATTTGATGTGGAC 58.121 37.500 0.00 0.00 0.00 4.02
1929 1980 4.028383 GCATAAATTTGATGTGGACGACG 58.972 43.478 0.00 0.00 0.00 5.12
1975 2026 3.766151 TCGATACAACGCTAGAGTTTGG 58.234 45.455 9.34 2.27 30.96 3.28
1985 2036 3.923461 CGCTAGAGTTTGGAGAGTTTGAG 59.077 47.826 0.00 0.00 0.00 3.02
1986 2037 4.249661 GCTAGAGTTTGGAGAGTTTGAGG 58.750 47.826 0.00 0.00 0.00 3.86
1987 2038 4.262678 GCTAGAGTTTGGAGAGTTTGAGGT 60.263 45.833 0.00 0.00 0.00 3.85
2233 3300 3.190874 GTGCATGGCAGTAGTTCTAGTC 58.809 50.000 0.00 0.00 40.08 2.59
2238 3305 2.260481 GGCAGTAGTTCTAGTCGTTGC 58.740 52.381 0.00 0.00 0.00 4.17
2240 3307 2.662156 GCAGTAGTTCTAGTCGTTGCAC 59.338 50.000 0.00 0.00 0.00 4.57
2259 3327 2.225019 CACAGAGCATCAAGAACCACAC 59.775 50.000 0.00 0.00 37.82 3.82
2263 3331 3.324846 AGAGCATCAAGAACCACACACTA 59.675 43.478 0.00 0.00 37.82 2.74
2279 3347 5.957796 CACACACTACGAAGAACAAAAACTC 59.042 40.000 0.00 0.00 0.00 3.01
2288 3356 6.090129 CGAAGAACAAAAACTCAGGAAACAA 58.910 36.000 0.00 0.00 0.00 2.83
2298 3366 6.850752 AACTCAGGAAACAAGAAAAGGAAA 57.149 33.333 0.00 0.00 0.00 3.13
2299 3367 7.423844 AACTCAGGAAACAAGAAAAGGAAAT 57.576 32.000 0.00 0.00 0.00 2.17
2305 3373 7.438160 CAGGAAACAAGAAAAGGAAATACAACC 59.562 37.037 0.00 0.00 0.00 3.77
2388 3468 5.006386 GGAGCATCTCTTTCCTTCAAAAGA 58.994 41.667 0.00 0.00 41.70 2.52
2390 3470 5.629125 AGCATCTCTTTCCTTCAAAAGACT 58.371 37.500 0.00 0.00 39.67 3.24
2474 3554 1.589803 AGTTGGGTTGTTGCGTAGAC 58.410 50.000 0.00 0.00 0.00 2.59
2486 3566 0.896226 GCGTAGACTCCAAACCCTCT 59.104 55.000 0.00 0.00 0.00 3.69
2495 3575 1.786441 TCCAAACCCTCTTCCACCAAT 59.214 47.619 0.00 0.00 0.00 3.16
2515 3595 9.408648 CACCAATCCTTAATAGTTATTGAGGTT 57.591 33.333 17.35 10.02 44.98 3.50
2568 3649 2.846193 TGAAAGGAGAACCAAACCTCG 58.154 47.619 0.00 0.00 38.94 4.63
2582 3663 2.597217 CTCGTGGGCAAAAGGGCA 60.597 61.111 0.00 0.00 45.66 5.36
2584 3665 4.362476 CGTGGGCAAAAGGGCAGC 62.362 66.667 0.00 0.00 45.66 5.25
2609 3690 0.178068 GAAAGATGGGCAGCCGACTA 59.822 55.000 5.00 0.00 0.00 2.59
2671 3752 2.125106 CCCTCGTGGCAAGCCTAC 60.125 66.667 12.96 7.95 36.94 3.18
2681 3762 3.400054 AAGCCTACCAGCCGTCCC 61.400 66.667 0.00 0.00 0.00 4.46
2693 6755 1.276989 AGCCGTCCCGATTTTGTTCTA 59.723 47.619 0.00 0.00 0.00 2.10
2769 6831 3.583383 GCAGTTGCGGCTCAGAAT 58.417 55.556 0.00 0.00 0.00 2.40
2777 6839 2.439156 GGCTCAGAATTGCGGCCT 60.439 61.111 0.00 0.00 38.76 5.19
2797 6859 5.250982 GCCTAAAAACTAAGCCTTGTAGGA 58.749 41.667 2.78 0.00 37.67 2.94
2838 6918 1.594833 CGAATGGAGTCGGGGACAA 59.405 57.895 0.00 0.00 37.37 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 2.815158 TCAGTGGCAGGAGTGTGTATA 58.185 47.619 0.00 0.00 0.00 1.47
84 85 2.374830 CTAGGGCGGATCAGTGGCAG 62.375 65.000 0.00 0.00 0.00 4.85
118 119 1.101635 TCCGATAGCCCGTGAGTCAG 61.102 60.000 0.00 0.00 0.00 3.51
126 127 0.592148 GTGTCTACTCCGATAGCCCG 59.408 60.000 0.00 0.00 0.00 6.13
133 134 1.304713 GGGGTGGTGTCTACTCCGA 60.305 63.158 0.00 0.00 32.43 4.55
136 137 2.040178 CTATGGGGGTGGTGTCTACTC 58.960 57.143 0.00 0.00 0.00 2.59
150 151 2.158957 TGCGCTAAGGTTTCTCTATGGG 60.159 50.000 9.73 0.00 0.00 4.00
171 172 1.410153 GGCGATCATGAGGGCAAATTT 59.590 47.619 18.94 0.00 0.00 1.82
176 177 1.146930 GAAGGCGATCATGAGGGCA 59.853 57.895 20.49 0.00 0.00 5.36
199 200 4.382320 CGGAAAACCCTCGGGCGA 62.382 66.667 0.82 0.00 39.32 5.54
225 226 1.108132 ACTAGCCTAGTAGCACGGGC 61.108 60.000 0.00 0.00 40.34 6.13
253 254 9.961265 CACGATGTAACTAAATATACTTGGAGA 57.039 33.333 0.00 0.00 0.00 3.71
275 276 1.797635 CACACACACATACATGCACGA 59.202 47.619 0.00 0.00 0.00 4.35
276 277 1.530720 ACACACACACATACATGCACG 59.469 47.619 0.00 0.00 0.00 5.34
297 308 1.955208 GCCATGACCGGAAAGACCATT 60.955 52.381 9.46 0.00 38.90 3.16
333 344 2.673368 GTGAACCACTCTAAGCAATCCG 59.327 50.000 0.00 0.00 0.00 4.18
357 369 3.883744 AAACCTGCGCGAGTCCCAG 62.884 63.158 12.10 7.05 0.00 4.45
368 380 1.081175 GGAGAGCGCAAAAACCTGC 60.081 57.895 11.47 0.00 39.04 4.85
385 397 2.218759 CGGAAAGAATTGACGCTATCGG 59.781 50.000 0.00 0.00 40.69 4.18
386 398 3.113322 TCGGAAAGAATTGACGCTATCG 58.887 45.455 0.00 0.00 42.43 2.92
391 403 3.370978 TCAATCTCGGAAAGAATTGACGC 59.629 43.478 0.00 0.00 37.61 5.19
394 406 4.943705 CCCTTCAATCTCGGAAAGAATTGA 59.056 41.667 0.00 0.00 37.61 2.57
405 417 2.799917 CGAGGTTAGCCCTTCAATCTCG 60.800 54.545 2.97 2.97 46.51 4.04
421 433 3.991367 AGAAAGAATGAAACGACGAGGT 58.009 40.909 0.00 0.00 0.00 3.85
509 521 1.734477 CAGCAACTCGTCACCTCCG 60.734 63.158 0.00 0.00 0.00 4.63
533 545 3.415087 CAGGAAGCCAGGGGGAGG 61.415 72.222 0.00 0.00 35.59 4.30
550 563 1.135139 TGAGCCATCAAGCTAGTCGTC 59.865 52.381 0.00 0.00 45.15 4.20
569 582 1.145531 TCAATGGCCCCCTACATGATG 59.854 52.381 0.00 0.00 0.00 3.07
726 755 1.999648 TGGAGCTGCCAACATTTTCT 58.000 45.000 1.53 0.00 45.87 2.52
787 817 0.036388 CTTACCTGCGTGTGGATGGT 60.036 55.000 0.00 0.00 35.05 3.55
788 818 1.369091 GCTTACCTGCGTGTGGATGG 61.369 60.000 0.00 0.00 0.00 3.51
837 867 0.674895 CTCGGGGCTTTTGTGGAGAG 60.675 60.000 0.00 0.00 0.00 3.20
935 965 1.967779 TGCTCTAGCCTTACACACACA 59.032 47.619 0.00 0.00 41.18 3.72
936 966 2.743636 TGCTCTAGCCTTACACACAC 57.256 50.000 0.00 0.00 41.18 3.82
937 967 2.612972 GCTTGCTCTAGCCTTACACACA 60.613 50.000 0.00 0.00 41.18 3.72
938 968 2.003301 GCTTGCTCTAGCCTTACACAC 58.997 52.381 0.00 0.00 41.18 3.82
939 969 1.404181 CGCTTGCTCTAGCCTTACACA 60.404 52.381 0.00 0.00 41.18 3.72
940 970 1.135083 TCGCTTGCTCTAGCCTTACAC 60.135 52.381 0.00 0.00 41.18 2.90
941 971 1.135139 CTCGCTTGCTCTAGCCTTACA 59.865 52.381 0.00 0.00 41.18 2.41
942 972 1.846541 CTCGCTTGCTCTAGCCTTAC 58.153 55.000 0.00 0.00 41.18 2.34
970 1000 6.484288 TCTTCTCTCAATTCTCTCAGTCTCT 58.516 40.000 0.00 0.00 0.00 3.10
1125 1155 0.886563 AAGAAGCATTGCAGGACAGC 59.113 50.000 11.91 0.00 0.00 4.40
1207 1237 5.049060 CAGCAAGACACGAGTAGCTAGATAT 60.049 44.000 0.00 0.00 31.73 1.63
1228 1258 1.660575 CAGCAGCAGCAACAACAGC 60.661 57.895 3.17 0.00 45.49 4.40
1229 1259 1.660575 GCAGCAGCAGCAACAACAG 60.661 57.895 4.63 0.00 45.49 3.16
1238 1271 2.019948 TCAGATAACAGCAGCAGCAG 57.980 50.000 3.17 0.00 45.49 4.24
1422 1455 5.243507 GGAATAGGTAGTAGGAGTAGGTTGC 59.756 48.000 0.00 0.00 0.00 4.17
1423 1456 6.371278 TGGAATAGGTAGTAGGAGTAGGTTG 58.629 44.000 0.00 0.00 0.00 3.77
1424 1457 6.603110 TGGAATAGGTAGTAGGAGTAGGTT 57.397 41.667 0.00 0.00 0.00 3.50
1425 1458 6.800223 ATGGAATAGGTAGTAGGAGTAGGT 57.200 41.667 0.00 0.00 0.00 3.08
1426 1459 7.471890 AGAATGGAATAGGTAGTAGGAGTAGG 58.528 42.308 0.00 0.00 0.00 3.18
1427 1460 8.798402 CAAGAATGGAATAGGTAGTAGGAGTAG 58.202 40.741 0.00 0.00 0.00 2.57
1428 1461 8.287350 ACAAGAATGGAATAGGTAGTAGGAGTA 58.713 37.037 0.00 0.00 0.00 2.59
1429 1462 7.133483 ACAAGAATGGAATAGGTAGTAGGAGT 58.867 38.462 0.00 0.00 0.00 3.85
1430 1463 7.287927 TGACAAGAATGGAATAGGTAGTAGGAG 59.712 40.741 0.00 0.00 0.00 3.69
1431 1464 7.130099 TGACAAGAATGGAATAGGTAGTAGGA 58.870 38.462 0.00 0.00 0.00 2.94
1432 1465 7.361457 TGACAAGAATGGAATAGGTAGTAGG 57.639 40.000 0.00 0.00 0.00 3.18
1435 1468 6.353082 CCCTTGACAAGAATGGAATAGGTAGT 60.353 42.308 16.99 0.00 0.00 2.73
1441 1474 3.269381 AGGCCCTTGACAAGAATGGAATA 59.731 43.478 16.99 0.00 0.00 1.75
1446 1479 2.229784 GACAAGGCCCTTGACAAGAATG 59.770 50.000 29.74 0.63 43.42 2.67
1447 1480 2.108952 AGACAAGGCCCTTGACAAGAAT 59.891 45.455 29.74 5.28 43.42 2.40
1449 1482 1.140312 AGACAAGGCCCTTGACAAGA 58.860 50.000 29.74 0.00 43.42 3.02
1450 1483 1.882623 GAAGACAAGGCCCTTGACAAG 59.117 52.381 29.74 8.31 43.42 3.16
1451 1484 1.478654 GGAAGACAAGGCCCTTGACAA 60.479 52.381 29.74 0.00 43.42 3.18
1452 1485 0.110486 GGAAGACAAGGCCCTTGACA 59.890 55.000 29.74 0.00 43.42 3.58
1453 1486 0.402121 AGGAAGACAAGGCCCTTGAC 59.598 55.000 29.74 22.99 43.42 3.18
1454 1487 0.693049 GAGGAAGACAAGGCCCTTGA 59.307 55.000 29.74 0.00 43.42 3.02
1455 1488 0.322906 GGAGGAAGACAAGGCCCTTG 60.323 60.000 21.95 21.95 45.85 3.61
1456 1489 0.476611 AGGAGGAAGACAAGGCCCTT 60.477 55.000 0.00 0.00 0.00 3.95
1457 1490 0.476611 AAGGAGGAAGACAAGGCCCT 60.477 55.000 0.00 0.00 0.00 5.19
1458 1491 0.034960 GAAGGAGGAAGACAAGGCCC 60.035 60.000 0.00 0.00 0.00 5.80
1473 1513 0.471617 AGATTGGGATGCCGAGAAGG 59.528 55.000 0.00 0.00 44.97 3.46
1486 1526 0.852777 CGATTACGCCGTCAGATTGG 59.147 55.000 0.00 0.00 0.00 3.16
1639 1681 1.415659 CTCACCTGGATGAGGATGGAC 59.584 57.143 14.66 0.00 46.33 4.02
1796 1841 1.377202 TGGGTGAATCAGAAGGCGC 60.377 57.895 0.00 0.00 0.00 6.53
1929 1980 0.882927 TAACACACAAGCTCGTGCCC 60.883 55.000 4.26 0.00 40.73 5.36
1975 2026 1.149148 GAACGGCACCTCAAACTCTC 58.851 55.000 0.00 0.00 0.00 3.20
1985 2036 0.798776 CATGAGTGAAGAACGGCACC 59.201 55.000 0.00 0.00 35.67 5.01
1986 2037 1.728971 CTCATGAGTGAAGAACGGCAC 59.271 52.381 14.95 0.00 33.05 5.01
1987 2038 1.344438 ACTCATGAGTGAAGAACGGCA 59.656 47.619 27.37 0.00 40.75 5.69
2012 2064 6.698766 ACCGCGTATACAAAATAAAGAGTAGG 59.301 38.462 4.92 0.00 0.00 3.18
2060 2112 6.533723 TGGTATGCAAGATAAGTAACTGAACG 59.466 38.462 0.00 0.00 0.00 3.95
2147 2245 1.609239 CACCTGAGCCCTGGCAATA 59.391 57.895 11.38 0.00 44.88 1.90
2203 3228 1.250328 CTGCCATGCACCTTCAAGAA 58.750 50.000 0.00 0.00 33.79 2.52
2205 3230 1.741706 CTACTGCCATGCACCTTCAAG 59.258 52.381 0.00 0.00 33.79 3.02
2206 3231 1.073763 ACTACTGCCATGCACCTTCAA 59.926 47.619 0.00 0.00 33.79 2.69
2207 3232 0.692476 ACTACTGCCATGCACCTTCA 59.308 50.000 0.00 0.00 33.79 3.02
2208 3233 1.740025 GAACTACTGCCATGCACCTTC 59.260 52.381 0.00 0.00 33.79 3.46
2209 3234 1.352352 AGAACTACTGCCATGCACCTT 59.648 47.619 0.00 0.00 33.79 3.50
2238 3305 2.225019 GTGTGGTTCTTGATGCTCTGTG 59.775 50.000 0.00 0.00 0.00 3.66
2240 3307 2.225019 GTGTGTGGTTCTTGATGCTCTG 59.775 50.000 0.00 0.00 0.00 3.35
2259 3327 5.522460 TCCTGAGTTTTTGTTCTTCGTAGTG 59.478 40.000 0.00 0.00 0.00 2.74
2263 3331 5.182380 TGTTTCCTGAGTTTTTGTTCTTCGT 59.818 36.000 0.00 0.00 0.00 3.85
2279 3347 7.438160 GGTTGTATTTCCTTTTCTTGTTTCCTG 59.562 37.037 0.00 0.00 0.00 3.86
2288 3356 5.454966 AGTGTGGGTTGTATTTCCTTTTCT 58.545 37.500 0.00 0.00 0.00 2.52
2298 3366 5.243207 GCTACTGTTTAGTGTGGGTTGTAT 58.757 41.667 0.00 0.00 37.78 2.29
2299 3367 4.503643 GGCTACTGTTTAGTGTGGGTTGTA 60.504 45.833 0.00 0.00 37.78 2.41
2305 3373 2.567615 AGGAGGCTACTGTTTAGTGTGG 59.432 50.000 0.00 0.00 37.78 4.17
2388 3468 8.140112 TCTTTAGAAAGAGAGAAATAGGCAGT 57.860 34.615 0.46 0.00 39.95 4.40
2474 3554 0.771127 TGGTGGAAGAGGGTTTGGAG 59.229 55.000 0.00 0.00 0.00 3.86
2486 3566 9.627123 CTCAATAACTATTAAGGATTGGTGGAA 57.373 33.333 0.00 0.00 33.86 3.53
2495 3575 8.325787 TGCTTCAACCTCAATAACTATTAAGGA 58.674 33.333 5.76 0.00 33.64 3.36
2568 3649 2.919328 AGCTGCCCTTTTGCCCAC 60.919 61.111 0.00 0.00 0.00 4.61
2582 3663 2.444421 CTGCCCATCTTTCTTTGAGCT 58.556 47.619 0.00 0.00 0.00 4.09
2584 3665 1.475682 GGCTGCCCATCTTTCTTTGAG 59.524 52.381 7.66 0.00 0.00 3.02
2609 3690 5.010415 TGCACGTTCTATGATCAGATCATCT 59.990 40.000 26.35 10.11 46.62 2.90
2693 6755 5.520748 AATTCCACCTCTGGTTATTGTCT 57.479 39.130 0.00 0.00 38.90 3.41
2769 6831 1.542472 GGCTTAGTTTTTAGGCCGCAA 59.458 47.619 0.00 0.00 33.30 4.85
2777 6839 6.235664 CACCTCCTACAAGGCTTAGTTTTTA 58.764 40.000 0.00 0.00 40.34 1.52
2797 6859 4.021925 GGTTCTCCGCTGCCACCT 62.022 66.667 0.00 0.00 0.00 4.00
2838 6918 2.899900 TCCAACACATAGTGCTCTCTGT 59.100 45.455 1.33 1.33 36.98 3.41


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

AutoCloner maintained by Alex Coulton.