Multiple sequence alignment - TraesCS1D01G043900

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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 TraesCS1D01G043900 chr1D 100.000 2417 0 0 1 2417 22902199 22904615 0.000000e+00 4464.0
1 TraesCS1D01G043900 chr1D 85.890 163 17 6 2123 2283 22977766 22977924 4.130000e-38 169.0
2 TraesCS1D01G043900 chr1D 94.340 106 6 0 2133 2238 22883033 22883138 1.920000e-36 163.0
3 TraesCS1D01G043900 chr1D 94.286 105 5 1 2132 2236 22983194 22983297 2.490000e-35 159.0
4 TraesCS1D01G043900 chr1A 88.429 1426 78 46 575 1958 24076970 24078350 0.000000e+00 1639.0
5 TraesCS1D01G043900 chr1A 86.807 523 32 19 4 504 24076380 24076887 1.260000e-152 549.0
6 TraesCS1D01G043900 chr1A 87.059 340 22 11 1957 2282 24078391 24078722 4.910000e-97 364.0
7 TraesCS1D01G043900 chr1A 88.050 159 10 6 2132 2283 24311635 24311791 1.910000e-41 180.0
8 TraesCS1D01G043900 chr1A 94.231 104 4 2 2133 2235 23965651 23965753 8.950000e-35 158.0
9 TraesCS1D01G043900 chr1B 85.148 1387 84 66 604 1958 39310809 39312105 0.000000e+00 1308.0
10 TraesCS1D01G043900 chr1B 83.230 483 27 20 1957 2417 39312149 39312599 6.260000e-106 394.0
11 TraesCS1D01G043900 chr1B 87.546 273 18 6 242 505 39310441 39310706 3.910000e-78 302.0
12 TraesCS1D01G043900 chr1B 89.157 166 12 4 2123 2282 38915112 38914947 4.070000e-48 202.0
13 TraesCS1D01G043900 chr1B 93.077 130 6 2 2145 2271 39386996 39387125 1.140000e-43 187.0
14 TraesCS1D01G043900 chr1B 84.328 134 7 5 2295 2417 38920832 38920702 4.220000e-23 119.0
15 TraesCS1D01G043900 chr1B 96.610 59 2 0 1 59 39310156 39310214 5.500000e-17 99.0
16 TraesCS1D01G043900 chr1B 84.507 71 4 5 2347 2417 38915020 38914957 2.010000e-06 63.9


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 TraesCS1D01G043900 chr1D 22902199 22904615 2416 False 4464.000000 4464 100.000000 1 2417 1 chr1D.!!$F2 2416
1 TraesCS1D01G043900 chr1A 24076380 24078722 2342 False 850.666667 1639 87.431667 4 2282 3 chr1A.!!$F3 2278
2 TraesCS1D01G043900 chr1B 39310156 39312599 2443 False 525.750000 1308 88.133500 1 2417 4 chr1B.!!$F2 2416

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
323 404 0.17915 GCGTGAAGCCAACAACAACA 60.179 50.0 0.0 0.0 40.81 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1948 0.108804 ATACACTCAACGACCAGGCG 60.109 55.0 0.0 0.0 37.29 5.52 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
30 31 2.369394 CCAGCCTAAACTCATTGACCC 58.631 52.381 0.00 0.00 0.00 4.46
67 93 6.088173 TCAAATCAAAGATCAATCACAAGCG 58.912 36.000 0.00 0.00 0.00 4.68
72 98 3.482722 AGATCAATCACAAGCGCAAAG 57.517 42.857 11.47 0.19 0.00 2.77
83 114 4.135570 CGCAAAGCAATCCACACG 57.864 55.556 0.00 0.00 0.00 4.49
99 130 2.535984 CACACGAGTTCTGACTTGTCAC 59.464 50.000 0.00 0.00 45.46 3.67
106 137 1.709578 TCTGACTTGTCACCAGCTCT 58.290 50.000 0.00 0.00 0.00 4.09
116 147 1.534959 ACCAGCTCTGCTCTGACCA 60.535 57.895 0.00 0.00 36.40 4.02
119 150 1.339824 CCAGCTCTGCTCTGACCATTT 60.340 52.381 0.00 0.00 36.40 2.32
179 211 4.759516 TTAAGAAAGAAAGCCGCGAAAT 57.240 36.364 8.23 0.00 0.00 2.17
202 255 1.484227 TTCGTTCGGTGCGTGTGAAG 61.484 55.000 0.00 0.00 0.00 3.02
210 263 1.005037 TGCGTGTGAAGGAATCGCT 60.005 52.632 9.08 0.00 45.69 4.93
216 273 1.092345 GTGAAGGAATCGCTCTGGCC 61.092 60.000 0.00 0.00 35.60 5.36
322 403 2.577225 GCGTGAAGCCAACAACAAC 58.423 52.632 0.00 0.00 40.81 3.32
323 404 0.179150 GCGTGAAGCCAACAACAACA 60.179 50.000 0.00 0.00 40.81 3.33
324 405 1.544686 CGTGAAGCCAACAACAACAC 58.455 50.000 0.00 0.00 0.00 3.32
365 446 1.201965 GCCAGCGTTTTCTGAATCTCG 60.202 52.381 0.00 0.00 36.19 4.04
375 456 4.488126 TTCTGAATCTCGCCTTTTTGTG 57.512 40.909 0.00 0.00 0.00 3.33
385 466 2.412847 CGCCTTTTTGTGCTGCTACTAC 60.413 50.000 0.00 0.00 0.00 2.73
386 467 2.814336 GCCTTTTTGTGCTGCTACTACT 59.186 45.455 0.00 0.00 0.00 2.57
387 468 4.000988 GCCTTTTTGTGCTGCTACTACTA 58.999 43.478 0.00 0.00 0.00 1.82
389 470 4.093556 CCTTTTTGTGCTGCTACTACTAGC 59.906 45.833 0.00 0.00 45.19 3.42
391 472 5.654603 TTTTGTGCTGCTACTACTAGCTA 57.345 39.130 0.00 0.00 45.20 3.32
392 473 4.902443 TTGTGCTGCTACTACTAGCTAG 57.098 45.455 19.44 19.44 45.20 3.42
393 474 2.619177 TGTGCTGCTACTACTAGCTAGC 59.381 50.000 20.91 6.62 45.20 3.42
394 475 2.882137 GTGCTGCTACTACTAGCTAGCT 59.118 50.000 23.12 23.12 45.20 3.32
395 476 4.066490 GTGCTGCTACTACTAGCTAGCTA 58.934 47.826 22.85 22.85 45.20 3.32
396 477 4.066490 TGCTGCTACTACTAGCTAGCTAC 58.934 47.826 20.67 9.58 45.20 3.58
397 478 3.437741 GCTGCTACTACTAGCTAGCTACC 59.562 52.174 20.67 5.37 45.20 3.18
451 536 4.129737 GCAGGCAGGCGTCTCGTA 62.130 66.667 0.00 0.00 0.00 3.43
498 583 1.152830 GGCCTCCAACAACCTGGAA 59.847 57.895 0.00 0.00 44.97 3.53
505 590 1.545428 CCAACAACCTGGAAGCTAGCA 60.545 52.381 18.83 0.00 38.96 3.49
508 593 1.021390 CAACCTGGAAGCTAGCACCG 61.021 60.000 18.83 14.45 0.00 4.94
509 594 1.481056 AACCTGGAAGCTAGCACCGT 61.481 55.000 18.83 10.87 0.00 4.83
510 595 1.448540 CCTGGAAGCTAGCACCGTG 60.449 63.158 18.83 14.91 0.00 4.94
512 597 1.888436 CTGGAAGCTAGCACCGTGGA 61.888 60.000 18.83 3.35 0.00 4.02
537 648 1.852895 GTAGCTCATACGCAAACCTCG 59.147 52.381 0.00 0.00 0.00 4.63
539 650 1.067142 AGCTCATACGCAAACCTCGAA 60.067 47.619 0.00 0.00 0.00 3.71
544 655 5.365403 TCATACGCAAACCTCGAATTTTT 57.635 34.783 0.00 0.00 0.00 1.94
567 678 8.725405 TTTTATCGCTAAACAATGGAGTATCA 57.275 30.769 0.00 0.00 36.25 2.15
568 679 7.709269 TTATCGCTAAACAATGGAGTATCAC 57.291 36.000 0.00 0.00 36.25 3.06
569 680 4.109766 TCGCTAAACAATGGAGTATCACG 58.890 43.478 0.00 0.00 36.25 4.35
570 681 4.109766 CGCTAAACAATGGAGTATCACGA 58.890 43.478 0.00 0.00 36.25 4.35
571 682 4.207224 CGCTAAACAATGGAGTATCACGAG 59.793 45.833 0.00 0.00 36.25 4.18
572 683 4.025647 GCTAAACAATGGAGTATCACGAGC 60.026 45.833 0.00 0.00 36.25 5.03
573 684 2.209838 ACAATGGAGTATCACGAGCG 57.790 50.000 0.00 0.00 36.25 5.03
596 707 1.064946 CCGGCTTCTACTCGAGCTG 59.935 63.158 13.61 5.58 0.00 4.24
597 708 1.377366 CCGGCTTCTACTCGAGCTGA 61.377 60.000 13.61 8.16 35.84 4.26
601 712 3.142951 GGCTTCTACTCGAGCTGATAGA 58.857 50.000 13.61 9.33 0.00 1.98
602 713 3.756434 GGCTTCTACTCGAGCTGATAGAT 59.244 47.826 13.61 0.00 0.00 1.98
604 715 5.064707 GGCTTCTACTCGAGCTGATAGATAG 59.935 48.000 13.61 12.08 0.00 2.08
605 716 5.447279 GCTTCTACTCGAGCTGATAGATAGC 60.447 48.000 13.61 16.78 41.43 2.97
620 731 7.908453 TGATAGATAGCTAGCTAGTCAGTGTA 58.092 38.462 27.42 14.48 34.18 2.90
622 733 4.992319 AGATAGCTAGCTAGTCAGTGTACG 59.008 45.833 27.42 0.00 31.45 3.67
624 735 4.134379 AGCTAGCTAGTCAGTGTACGTA 57.866 45.455 17.69 0.00 0.00 3.57
625 736 4.706035 AGCTAGCTAGTCAGTGTACGTAT 58.294 43.478 17.69 0.00 0.00 3.06
627 738 6.465948 AGCTAGCTAGTCAGTGTACGTATAT 58.534 40.000 17.69 0.00 0.00 0.86
629 740 6.183360 GCTAGCTAGTCAGTGTACGTATATCC 60.183 46.154 21.62 0.00 0.00 2.59
651 762 1.793258 CTAGCTAGCGCGTAGGAGTA 58.207 55.000 8.05 0.00 42.32 2.59
652 763 2.141517 CTAGCTAGCGCGTAGGAGTAA 58.858 52.381 8.05 0.00 42.32 2.24
653 764 0.945813 AGCTAGCGCGTAGGAGTAAG 59.054 55.000 9.55 0.00 42.32 2.34
654 765 0.942962 GCTAGCGCGTAGGAGTAAGA 59.057 55.000 8.43 0.00 0.00 2.10
672 784 7.363705 GGAGTAAGAAGGAGGAGTAGTAAAACC 60.364 44.444 0.00 0.00 0.00 3.27
726 843 2.546494 CCGGCCCATTTCATCGCTC 61.546 63.158 0.00 0.00 0.00 5.03
829 958 1.115930 CGTCCCCTCCTCCACCATAG 61.116 65.000 0.00 0.00 0.00 2.23
930 1075 3.854669 CCGGCTGGTCTGGCTAGG 61.855 72.222 2.29 0.00 33.73 3.02
951 1096 0.970937 AGCTAGCTACCGCCTTGTCA 60.971 55.000 17.69 0.00 36.60 3.58
958 1103 2.292794 TACCGCCTTGTCATCGGCTC 62.293 60.000 10.80 0.00 46.49 4.70
959 1104 2.892425 CGCCTTGTCATCGGCTCC 60.892 66.667 10.80 0.00 44.11 4.70
960 1105 2.586792 GCCTTGTCATCGGCTCCT 59.413 61.111 6.45 0.00 42.98 3.69
961 1106 1.522580 GCCTTGTCATCGGCTCCTC 60.523 63.158 6.45 0.00 42.98 3.71
962 1107 1.227089 CCTTGTCATCGGCTCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
1239 1389 0.482446 ATCAACACCACCACCACCAT 59.518 50.000 0.00 0.00 0.00 3.55
1245 1401 1.603455 CCACCACCACCATCACCAC 60.603 63.158 0.00 0.00 0.00 4.16
1386 1542 1.587054 CGTGGAGAAGAGGCTCGTT 59.413 57.895 9.22 3.88 35.74 3.85
1389 1545 0.541998 TGGAGAAGAGGCTCGTTCCA 60.542 55.000 24.27 24.27 35.74 3.53
1419 1575 1.003355 CCCGTTGCATCACTGAGGT 60.003 57.895 0.00 0.00 0.00 3.85
1420 1576 0.606401 CCCGTTGCATCACTGAGGTT 60.606 55.000 0.00 0.00 0.00 3.50
1422 1578 1.511850 CGTTGCATCACTGAGGTTCA 58.488 50.000 0.00 0.00 0.00 3.18
1423 1579 2.079158 CGTTGCATCACTGAGGTTCAT 58.921 47.619 0.00 0.00 0.00 2.57
1424 1580 2.159612 CGTTGCATCACTGAGGTTCATG 60.160 50.000 0.00 0.00 0.00 3.07
1425 1581 2.118313 TGCATCACTGAGGTTCATGG 57.882 50.000 0.00 0.00 0.00 3.66
1426 1582 0.737219 GCATCACTGAGGTTCATGGC 59.263 55.000 0.00 0.00 0.00 4.40
1427 1583 1.386533 CATCACTGAGGTTCATGGCC 58.613 55.000 0.00 0.00 0.00 5.36
1430 1595 3.197790 CTGAGGTTCATGGCCGCG 61.198 66.667 0.00 0.00 0.00 6.46
1477 1642 9.904198 TTTTTCATGTACTTATCCTGATCATCA 57.096 29.630 0.00 0.00 0.00 3.07
1578 1746 6.502136 TTGTGTTGTTGTTGTTGAGTATGA 57.498 33.333 0.00 0.00 0.00 2.15
1579 1747 6.502136 TGTGTTGTTGTTGTTGAGTATGAA 57.498 33.333 0.00 0.00 0.00 2.57
1580 1748 6.914259 TGTGTTGTTGTTGTTGAGTATGAAA 58.086 32.000 0.00 0.00 0.00 2.69
1581 1749 7.542890 TGTGTTGTTGTTGTTGAGTATGAAAT 58.457 30.769 0.00 0.00 0.00 2.17
1582 1750 7.700234 TGTGTTGTTGTTGTTGAGTATGAAATC 59.300 33.333 0.00 0.00 0.00 2.17
1583 1751 7.915397 GTGTTGTTGTTGTTGAGTATGAAATCT 59.085 33.333 0.00 0.00 0.00 2.40
1585 1753 8.958043 GTTGTTGTTGTTGAGTATGAAATCTTC 58.042 33.333 0.00 0.00 0.00 2.87
1587 1755 7.502226 TGTTGTTGTTGAGTATGAAATCTTCCT 59.498 33.333 0.00 0.00 0.00 3.36
1588 1756 7.672983 TGTTGTTGAGTATGAAATCTTCCTC 57.327 36.000 0.00 0.00 0.00 3.71
1589 1757 7.453393 TGTTGTTGAGTATGAAATCTTCCTCT 58.547 34.615 0.00 0.00 0.00 3.69
1690 1870 3.689161 GCAGGTGACATTTGCATGTACTA 59.311 43.478 8.70 0.00 44.22 1.82
1692 1872 4.937620 CAGGTGACATTTGCATGTACTACT 59.062 41.667 0.00 0.00 44.22 2.57
1693 1873 4.937620 AGGTGACATTTGCATGTACTACTG 59.062 41.667 0.00 0.00 44.22 2.74
1694 1874 4.695455 GGTGACATTTGCATGTACTACTGT 59.305 41.667 0.00 0.00 44.22 3.55
1696 1876 6.538742 GGTGACATTTGCATGTACTACTGTAT 59.461 38.462 0.00 0.00 44.22 2.29
1698 1878 9.093970 GTGACATTTGCATGTACTACTGTATAA 57.906 33.333 0.00 0.00 44.22 0.98
1735 1916 9.561069 AGTGATCTGTAATTACTTCACTTTGTT 57.439 29.630 26.37 14.99 37.85 2.83
1737 1918 9.778741 TGATCTGTAATTACTTCACTTTGTTCT 57.221 29.630 16.33 0.00 0.00 3.01
1752 1933 6.701400 CACTTTGTTCTTTTTACTGATTGGGG 59.299 38.462 0.00 0.00 0.00 4.96
1769 1950 1.076332 GGGAACCGATGTATATGCGC 58.924 55.000 0.00 0.00 40.86 6.09
1779 1960 0.859232 GTATATGCGCCTGGTCGTTG 59.141 55.000 4.18 0.00 0.00 4.10
1903 2094 2.167693 ACACGAACAGAAGGAGTGAACA 59.832 45.455 0.69 0.00 36.71 3.18
2106 2345 3.181540 CGAGTAGCAAAACATCTCACGTG 60.182 47.826 9.94 9.94 0.00 4.49
2228 2467 0.331278 TCAAATCCCGGCAATGGAGT 59.669 50.000 0.00 0.00 34.80 3.85
2229 2468 1.562008 TCAAATCCCGGCAATGGAGTA 59.438 47.619 0.00 0.00 34.80 2.59
2279 2529 9.672086 GCTGCGTTTTATTTTGAATATATACCA 57.328 29.630 0.00 0.00 0.00 3.25
2310 2560 6.165577 GGCAATGGAGCATTTCTTTTTCTTA 58.834 36.000 0.00 0.00 31.05 2.10
2311 2561 6.091305 GGCAATGGAGCATTTCTTTTTCTTAC 59.909 38.462 0.00 0.00 31.05 2.34
2312 2562 6.870439 GCAATGGAGCATTTCTTTTTCTTACT 59.130 34.615 0.00 0.00 31.05 2.24
2342 2592 4.384940 TCTGCAGTGTGCTGTGTTTTATA 58.615 39.130 14.67 0.00 45.31 0.98
2343 2593 4.213270 TCTGCAGTGTGCTGTGTTTTATAC 59.787 41.667 14.67 0.00 45.31 1.47
2344 2594 3.252215 TGCAGTGTGCTGTGTTTTATACC 59.748 43.478 0.00 0.00 45.31 2.73
2345 2595 3.365969 GCAGTGTGCTGTGTTTTATACCC 60.366 47.826 0.00 0.00 44.32 3.69
2349 2599 5.183140 AGTGTGCTGTGTTTTATACCCAATC 59.817 40.000 0.00 0.00 0.00 2.67
2350 2600 4.461081 TGTGCTGTGTTTTATACCCAATCC 59.539 41.667 0.00 0.00 0.00 3.01
2351 2601 4.020543 TGCTGTGTTTTATACCCAATCCC 58.979 43.478 0.00 0.00 0.00 3.85
2352 2602 3.066203 GCTGTGTTTTATACCCAATCCCG 59.934 47.826 0.00 0.00 0.00 5.14
2353 2603 3.622630 TGTGTTTTATACCCAATCCCGG 58.377 45.455 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 91 2.082366 CGTGTGGATTGCTTTGCGC 61.082 57.895 0.00 0.00 39.77 6.09
67 93 0.593128 ACTCGTGTGGATTGCTTTGC 59.407 50.000 0.00 0.00 0.00 3.68
72 98 1.461127 GTCAGAACTCGTGTGGATTGC 59.539 52.381 0.00 0.00 0.00 3.56
83 114 2.139118 GCTGGTGACAAGTCAGAACTC 58.861 52.381 2.62 0.00 42.06 3.01
99 130 0.252479 AATGGTCAGAGCAGAGCTGG 59.748 55.000 8.56 0.00 39.88 4.85
106 137 3.673902 TCGAAATGAAATGGTCAGAGCA 58.326 40.909 4.40 4.40 40.43 4.26
116 147 3.000322 GCGAGACGACATCGAAATGAAAT 60.000 43.478 8.54 0.00 42.76 2.17
119 150 1.135517 TGCGAGACGACATCGAAATGA 60.136 47.619 8.54 0.00 42.76 2.57
179 211 2.278726 ACGCACCGAACGAACGAA 60.279 55.556 0.14 0.00 35.09 3.85
187 224 0.250124 ATTCCTTCACACGCACCGAA 60.250 50.000 0.00 0.00 0.00 4.30
190 227 1.787847 CGATTCCTTCACACGCACC 59.212 57.895 0.00 0.00 0.00 5.01
210 263 1.675310 CATGTTCAAGCCGGCCAGA 60.675 57.895 26.15 19.25 0.00 3.86
216 273 1.926511 GAGGTGCCATGTTCAAGCCG 61.927 60.000 0.00 0.00 0.00 5.52
276 346 2.335712 CCCGGCTTTGACTTCCAGC 61.336 63.158 0.00 0.00 0.00 4.85
318 399 0.741574 TGAAGGAACGTGCGTGTTGT 60.742 50.000 0.00 0.00 30.75 3.32
321 402 0.179094 TCTTGAAGGAACGTGCGTGT 60.179 50.000 0.00 0.00 0.00 4.49
322 403 0.508641 CTCTTGAAGGAACGTGCGTG 59.491 55.000 0.00 0.00 0.00 5.34
323 404 1.222115 GCTCTTGAAGGAACGTGCGT 61.222 55.000 0.00 0.00 0.00 5.24
324 405 1.493311 GCTCTTGAAGGAACGTGCG 59.507 57.895 0.00 0.00 0.00 5.34
365 446 2.814336 AGTAGTAGCAGCACAAAAAGGC 59.186 45.455 0.00 0.00 0.00 4.35
385 466 4.946478 ATTCAAGGTGGTAGCTAGCTAG 57.054 45.455 24.78 16.84 0.00 3.42
386 467 5.396436 GGAAATTCAAGGTGGTAGCTAGCTA 60.396 44.000 20.67 20.67 0.00 3.32
387 468 4.518249 GAAATTCAAGGTGGTAGCTAGCT 58.482 43.478 23.12 23.12 0.00 3.32
389 470 5.104259 AGGAAATTCAAGGTGGTAGCTAG 57.896 43.478 0.00 0.00 0.00 3.42
391 472 4.082125 CAAGGAAATTCAAGGTGGTAGCT 58.918 43.478 0.00 0.00 0.00 3.32
392 473 3.367395 GCAAGGAAATTCAAGGTGGTAGC 60.367 47.826 0.00 0.00 0.00 3.58
393 474 3.826157 TGCAAGGAAATTCAAGGTGGTAG 59.174 43.478 0.00 0.00 0.00 3.18
394 475 3.838565 TGCAAGGAAATTCAAGGTGGTA 58.161 40.909 0.00 0.00 0.00 3.25
395 476 2.676748 TGCAAGGAAATTCAAGGTGGT 58.323 42.857 0.00 0.00 0.00 4.16
396 477 3.592059 CATGCAAGGAAATTCAAGGTGG 58.408 45.455 0.00 0.00 0.00 4.61
397 478 3.258872 TCCATGCAAGGAAATTCAAGGTG 59.741 43.478 8.54 0.00 33.93 4.00
451 536 0.612174 TCTCAAGTCTAGCGGCAGGT 60.612 55.000 1.45 0.00 0.00 4.00
498 583 2.190756 GTACTCCACGGTGCTAGCT 58.809 57.895 17.23 0.00 0.00 3.32
508 593 3.250464 CGTATGAGCTACGTACTCCAC 57.750 52.381 17.08 14.36 46.46 4.02
544 655 6.419710 CGTGATACTCCATTGTTTAGCGATAA 59.580 38.462 0.00 0.00 0.00 1.75
545 656 5.918576 CGTGATACTCCATTGTTTAGCGATA 59.081 40.000 0.00 0.00 0.00 2.92
546 657 4.745125 CGTGATACTCCATTGTTTAGCGAT 59.255 41.667 0.00 0.00 0.00 4.58
547 658 4.109766 CGTGATACTCCATTGTTTAGCGA 58.890 43.478 0.00 0.00 0.00 4.93
548 659 4.109766 TCGTGATACTCCATTGTTTAGCG 58.890 43.478 0.00 0.00 0.00 4.26
549 660 4.025647 GCTCGTGATACTCCATTGTTTAGC 60.026 45.833 0.00 0.00 0.00 3.09
550 661 4.207224 CGCTCGTGATACTCCATTGTTTAG 59.793 45.833 0.00 0.00 0.00 1.85
554 665 1.476891 ACGCTCGTGATACTCCATTGT 59.523 47.619 0.00 0.00 0.00 2.71
555 666 2.209838 ACGCTCGTGATACTCCATTG 57.790 50.000 0.00 0.00 0.00 2.82
556 667 2.961526 AACGCTCGTGATACTCCATT 57.038 45.000 0.00 0.00 0.00 3.16
557 668 2.481449 GGAAACGCTCGTGATACTCCAT 60.481 50.000 0.00 0.00 0.00 3.41
558 669 1.135199 GGAAACGCTCGTGATACTCCA 60.135 52.381 0.00 0.00 0.00 3.86
559 670 1.557651 GGAAACGCTCGTGATACTCC 58.442 55.000 0.00 0.00 0.00 3.85
560 671 1.557651 GGGAAACGCTCGTGATACTC 58.442 55.000 0.00 0.00 0.00 2.59
561 672 0.179145 CGGGAAACGCTCGTGATACT 60.179 55.000 0.00 0.00 34.82 2.12
562 673 1.143969 CCGGGAAACGCTCGTGATAC 61.144 60.000 0.00 0.00 42.52 2.24
563 674 1.140161 CCGGGAAACGCTCGTGATA 59.860 57.895 0.00 0.00 42.52 2.15
564 675 2.125673 CCGGGAAACGCTCGTGAT 60.126 61.111 0.00 0.00 42.52 3.06
567 678 4.309950 AAGCCGGGAAACGCTCGT 62.310 61.111 2.18 0.00 42.52 4.18
568 679 2.552585 TAGAAGCCGGGAAACGCTCG 62.553 60.000 2.18 0.00 42.52 5.03
569 680 1.082679 GTAGAAGCCGGGAAACGCTC 61.083 60.000 2.18 0.00 42.52 5.03
570 681 1.079336 GTAGAAGCCGGGAAACGCT 60.079 57.895 2.18 0.00 42.52 5.07
571 682 1.079336 AGTAGAAGCCGGGAAACGC 60.079 57.895 2.18 0.00 42.52 4.84
572 683 0.801067 CGAGTAGAAGCCGGGAAACG 60.801 60.000 2.18 0.00 43.80 3.60
573 684 0.529378 TCGAGTAGAAGCCGGGAAAC 59.471 55.000 2.18 0.00 0.00 2.78
596 707 7.009815 CGTACACTGACTAGCTAGCTATCTATC 59.990 44.444 24.36 18.21 0.00 2.08
597 708 6.814644 CGTACACTGACTAGCTAGCTATCTAT 59.185 42.308 24.36 10.78 0.00 1.98
601 712 4.706035 ACGTACACTGACTAGCTAGCTAT 58.294 43.478 24.36 14.44 0.00 2.97
602 713 4.134379 ACGTACACTGACTAGCTAGCTA 57.866 45.455 22.85 22.85 0.00 3.32
604 715 6.183360 GGATATACGTACACTGACTAGCTAGC 60.183 46.154 20.91 6.62 0.00 3.42
605 716 6.872547 TGGATATACGTACACTGACTAGCTAG 59.127 42.308 19.44 19.44 0.00 3.42
606 717 6.762333 TGGATATACGTACACTGACTAGCTA 58.238 40.000 0.00 0.00 0.00 3.32
607 718 5.618236 TGGATATACGTACACTGACTAGCT 58.382 41.667 0.00 0.00 0.00 3.32
608 719 5.617308 GCTGGATATACGTACACTGACTAGC 60.617 48.000 0.00 2.44 0.00 3.42
620 731 2.678836 CGCTAGCTAGCTGGATATACGT 59.321 50.000 36.02 1.47 46.85 3.57
622 733 2.539953 CGCGCTAGCTAGCTGGATATAC 60.540 54.545 36.02 17.57 46.85 1.47
624 735 0.453793 CGCGCTAGCTAGCTGGATAT 59.546 55.000 36.02 4.62 46.85 1.63
625 736 0.889638 ACGCGCTAGCTAGCTGGATA 60.890 55.000 36.02 8.55 46.85 2.59
627 738 1.507974 CTACGCGCTAGCTAGCTGGA 61.508 60.000 36.02 25.92 46.85 3.86
629 740 1.081774 CCTACGCGCTAGCTAGCTG 60.082 63.158 36.02 30.07 46.85 4.24
647 758 7.546358 GGTTTTACTACTCCTCCTTCTTACTC 58.454 42.308 0.00 0.00 0.00 2.59
651 762 4.222366 CCGGTTTTACTACTCCTCCTTCTT 59.778 45.833 0.00 0.00 0.00 2.52
652 763 3.768215 CCGGTTTTACTACTCCTCCTTCT 59.232 47.826 0.00 0.00 0.00 2.85
653 764 3.513119 ACCGGTTTTACTACTCCTCCTTC 59.487 47.826 0.00 0.00 0.00 3.46
654 765 3.260128 CACCGGTTTTACTACTCCTCCTT 59.740 47.826 2.97 0.00 0.00 3.36
816 933 1.905215 CTATGGCCTATGGTGGAGGAG 59.095 57.143 3.32 0.00 35.99 3.69
930 1075 0.745468 ACAAGGCGGTAGCTAGCTAC 59.255 55.000 36.63 36.63 45.89 3.58
937 1082 1.883084 CCGATGACAAGGCGGTAGC 60.883 63.158 6.60 0.00 40.17 3.58
938 1083 1.883084 GCCGATGACAAGGCGGTAG 60.883 63.158 9.18 0.00 46.38 3.18
939 1084 2.185867 GCCGATGACAAGGCGGTA 59.814 61.111 9.18 0.00 46.38 4.02
968 1115 3.813724 GGCCTGGGGAGTCATGGG 61.814 72.222 0.00 0.00 0.00 4.00
1023 1170 3.965539 GAGGAGGACGACGACGGGA 62.966 68.421 12.58 0.00 44.46 5.14
1095 1242 4.742201 GAGCTTCCGCGCCTGACA 62.742 66.667 0.00 0.00 42.32 3.58
1181 1331 3.999297 GACGAGGGGTCGAGGCTCT 62.999 68.421 13.50 0.00 35.61 4.09
1245 1401 2.767536 GTGACCACCACGATGATGG 58.232 57.895 0.00 0.00 46.10 3.51
1293 1449 1.201647 CTCTGCCAGTTCCATTTGCTG 59.798 52.381 0.00 0.00 0.00 4.41
1345 1501 4.271816 CCGCGGGTCGATCTCCTG 62.272 72.222 20.10 7.89 41.67 3.86
1386 1542 3.961414 GGGTTCGGGCCTGTTGGA 61.961 66.667 12.43 0.00 34.57 3.53
1427 1583 4.569180 ATGGATGGAAGCCCCGCG 62.569 66.667 0.00 0.00 46.54 6.46
1430 1595 2.199535 CCCATGGATGGAAGCCCC 59.800 66.667 15.22 0.00 46.54 5.80
1493 1658 1.444933 TTTCTCCCTCTCCCTTGCAA 58.555 50.000 0.00 0.00 0.00 4.08
1557 1723 7.915397 AGATTTCATACTCAACAACAACAACAC 59.085 33.333 0.00 0.00 0.00 3.32
1578 1746 6.961360 AGAAACGGAAAAAGAGGAAGATTT 57.039 33.333 0.00 0.00 0.00 2.17
1579 1747 6.655425 CCTAGAAACGGAAAAAGAGGAAGATT 59.345 38.462 0.00 0.00 0.00 2.40
1580 1748 6.174049 CCTAGAAACGGAAAAAGAGGAAGAT 58.826 40.000 0.00 0.00 0.00 2.40
1581 1749 5.071384 ACCTAGAAACGGAAAAAGAGGAAGA 59.929 40.000 0.00 0.00 0.00 2.87
1582 1750 5.306394 ACCTAGAAACGGAAAAAGAGGAAG 58.694 41.667 0.00 0.00 0.00 3.46
1583 1751 5.300411 ACCTAGAAACGGAAAAAGAGGAA 57.700 39.130 0.00 0.00 0.00 3.36
1585 1753 4.820173 ACAACCTAGAAACGGAAAAAGAGG 59.180 41.667 0.00 0.00 0.00 3.69
1587 1755 4.818005 GGACAACCTAGAAACGGAAAAAGA 59.182 41.667 0.00 0.00 0.00 2.52
1588 1756 4.577283 TGGACAACCTAGAAACGGAAAAAG 59.423 41.667 0.00 0.00 37.04 2.27
1589 1757 4.525024 TGGACAACCTAGAAACGGAAAAA 58.475 39.130 0.00 0.00 37.04 1.94
1692 1872 9.836864 ACAGATCACTGCAAATAATCTTATACA 57.163 29.630 0.00 0.00 46.95 2.29
1724 1905 9.023967 CCAATCAGTAAAAAGAACAAAGTGAAG 57.976 33.333 0.00 0.00 0.00 3.02
1735 1916 4.076394 CGGTTCCCCAATCAGTAAAAAGA 58.924 43.478 0.00 0.00 0.00 2.52
1737 1918 4.101645 TCGGTTCCCCAATCAGTAAAAA 57.898 40.909 0.00 0.00 0.00 1.94
1738 1919 3.791953 TCGGTTCCCCAATCAGTAAAA 57.208 42.857 0.00 0.00 0.00 1.52
1752 1933 1.726791 CAGGCGCATATACATCGGTTC 59.273 52.381 10.83 0.00 0.00 3.62
1764 1945 2.434884 CTCAACGACCAGGCGCAT 60.435 61.111 10.83 0.00 33.86 4.73
1765 1946 3.923864 ACTCAACGACCAGGCGCA 61.924 61.111 10.83 0.00 33.86 6.09
1766 1947 2.758770 TACACTCAACGACCAGGCGC 62.759 60.000 0.00 0.00 33.86 6.53
1767 1948 0.108804 ATACACTCAACGACCAGGCG 60.109 55.000 0.00 0.00 37.29 5.52
1768 1949 1.732259 CAATACACTCAACGACCAGGC 59.268 52.381 0.00 0.00 0.00 4.85
1769 1950 1.732259 GCAATACACTCAACGACCAGG 59.268 52.381 0.00 0.00 0.00 4.45
1779 1960 2.368439 TGGGAGCAATGCAATACACTC 58.632 47.619 8.35 0.00 0.00 3.51
1859 2049 8.878769 GTGTTTATAAGGCCCAATACATTTTTG 58.121 33.333 0.00 0.00 0.00 2.44
1860 2050 7.762159 CGTGTTTATAAGGCCCAATACATTTTT 59.238 33.333 0.00 0.00 0.00 1.94
1861 2051 7.122948 TCGTGTTTATAAGGCCCAATACATTTT 59.877 33.333 0.00 0.00 0.00 1.82
1903 2094 1.340405 GGCCAGTCTGTCCATGAACAT 60.340 52.381 0.00 0.00 0.00 2.71
1995 2233 8.828751 TGGGGGTATACAAATACAATATACTCC 58.171 37.037 10.02 10.02 45.84 3.85
2001 2239 9.937876 TCATTTTGGGGGTATACAAATACAATA 57.062 29.630 5.01 0.00 39.90 1.90
2043 2281 9.778741 GGAGATATATTTAGTCATGGTTGTCAA 57.221 33.333 0.00 0.00 0.00 3.18
2074 2313 1.592400 TTGCTACTCGGTCCGTGGAG 61.592 60.000 19.33 19.33 34.86 3.86
2128 2367 7.639162 TCGTGACTACTTGAAAGATTCTTTC 57.361 36.000 25.61 25.61 0.00 2.62
2139 2378 5.147330 ACAATGGATTCGTGACTACTTGA 57.853 39.130 0.00 0.00 0.00 3.02
2140 2379 4.031765 CGACAATGGATTCGTGACTACTTG 59.968 45.833 0.00 0.00 0.00 3.16
2143 2382 3.508762 ACGACAATGGATTCGTGACTAC 58.491 45.455 0.00 0.00 46.41 2.73
2246 2496 0.386731 AATAAAACGCAGCACACCGC 60.387 50.000 0.00 0.00 42.91 5.68
2279 2529 0.397535 ATGCTCCATTGCCGGGATTT 60.398 50.000 2.18 0.00 33.04 2.17
2282 2532 1.000233 AAATGCTCCATTGCCGGGA 60.000 52.632 2.18 0.00 34.04 5.14
2284 2534 0.819582 AAGAAATGCTCCATTGCCGG 59.180 50.000 0.00 0.00 34.04 6.13
2327 2577 4.461081 GGATTGGGTATAAAACACAGCACA 59.539 41.667 0.00 0.00 44.08 4.57
2342 2592 2.043046 CCATTGCCGGGATTGGGT 60.043 61.111 24.74 0.00 0.00 4.51
2343 2593 1.829533 CTCCATTGCCGGGATTGGG 60.830 63.158 29.55 19.26 33.04 4.12
2344 2594 2.492773 GCTCCATTGCCGGGATTGG 61.493 63.158 26.04 26.04 33.04 3.16
2345 2595 2.492773 GGCTCCATTGCCGGGATTG 61.493 63.158 10.58 10.58 43.74 2.67
2375 2637 5.342259 GCACACCGCAGAAGTTTATAAAAAG 59.658 40.000 0.00 0.00 41.79 2.27
2376 2638 5.009210 AGCACACCGCAGAAGTTTATAAAAA 59.991 36.000 0.00 0.00 46.13 1.94
2377 2639 4.517453 AGCACACCGCAGAAGTTTATAAAA 59.483 37.500 0.00 0.00 46.13 1.52
2378 2640 4.069304 AGCACACCGCAGAAGTTTATAAA 58.931 39.130 0.00 0.00 46.13 1.40
2379 2641 3.435327 CAGCACACCGCAGAAGTTTATAA 59.565 43.478 0.00 0.00 46.13 0.98
2380 2642 3.000041 CAGCACACCGCAGAAGTTTATA 59.000 45.455 0.00 0.00 46.13 0.98
2393 2655 2.225491 TCAGAATAAAACGCAGCACACC 59.775 45.455 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.