Multiple sequence alignment - TraesCS1B01G193100

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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 TraesCS1B01G193100 chr1B 100.000 2660 0 0 1 2660 346167692 346170351 0.000000e+00 4913.0
1 TraesCS1B01G193100 chr1A 92.206 1822 119 18 847 2660 335830744 335832550 0.000000e+00 2556.0
2 TraesCS1B01G193100 chr1A 89.239 762 51 11 5 752 335828427 335829171 0.000000e+00 924.0
3 TraesCS1B01G193100 chr1A 96.552 58 2 0 1057 1114 47817214 47817157 2.180000e-16 97.1
4 TraesCS1B01G193100 chr1D 94.018 1538 69 14 847 2377 267380870 267379349 0.000000e+00 2309.0
5 TraesCS1B01G193100 chr1D 88.183 677 36 16 84 743 267385115 267384466 0.000000e+00 767.0
6 TraesCS1B01G193100 chr1D 87.008 254 19 11 2421 2660 267379354 267379101 9.380000e-70 274.0
7 TraesCS1B01G193100 chr1D 96.190 105 4 0 1439 1543 474916822 474916926 3.520000e-39 172.0
8 TraesCS1B01G193100 chr1D 90.265 113 8 3 1276 1386 474916703 474916814 7.670000e-31 145.0
9 TraesCS1B01G193100 chr1D 96.610 59 2 0 1058 1116 474916649 474916707 6.060000e-17 99.0
10 TraesCS1B01G193100 chr5A 87.356 174 12 7 1276 1448 37968033 37967869 9.720000e-45 191.0
11 TraesCS1B01G193100 chr5D 97.143 105 3 0 1439 1543 563593025 563593129 7.570000e-41 178.0
12 TraesCS1B01G193100 chr5D 96.190 105 4 0 1439 1543 213075134 213075030 3.520000e-39 172.0
13 TraesCS1B01G193100 chr5D 96.610 59 2 0 1058 1116 563592852 563592910 6.060000e-17 99.0
14 TraesCS1B01G193100 chr4D 97.143 105 3 0 1439 1543 348307230 348307126 7.570000e-41 178.0
15 TraesCS1B01G193100 chr4D 90.351 114 8 1 1276 1386 348307351 348307238 2.130000e-31 147.0
16 TraesCS1B01G193100 chr2D 97.143 105 3 0 1439 1543 33946003 33946107 7.570000e-41 178.0
17 TraesCS1B01G193100 chr2D 96.190 105 4 0 1439 1543 56188800 56188904 3.520000e-39 172.0
18 TraesCS1B01G193100 chr2D 96.610 59 2 0 1058 1116 33945836 33945894 6.060000e-17 99.0
19 TraesCS1B01G193100 chr2D 96.610 59 2 0 1058 1116 56188625 56188683 6.060000e-17 99.0
20 TraesCS1B01G193100 chr7D 96.154 104 4 0 1439 1542 293591779 293591676 1.270000e-38 171.0
21 TraesCS1B01G193100 chr7D 96.610 59 2 0 1058 1116 293591952 293591894 6.060000e-17 99.0
22 TraesCS1B01G193100 chr5B 92.793 111 8 0 1276 1386 45021655 45021765 7.620000e-36 161.0
23 TraesCS1B01G193100 chr2A 94.286 105 6 0 1282 1386 36029223 36029119 7.620000e-36 161.0
24 TraesCS1B01G193100 chr6A 90.090 111 11 0 1276 1386 41340222 41340332 7.670000e-31 145.0
25 TraesCS1B01G193100 chr3B 91.429 105 9 0 1282 1386 262837506 262837402 7.670000e-31 145.0
26 TraesCS1B01G193100 chr6D 96.610 59 2 0 1058 1116 263961488 263961546 6.060000e-17 99.0


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 TraesCS1B01G193100 chr1B 346167692 346170351 2659 False 4913.000000 4913 100.000000 1 2660 1 chr1B.!!$F1 2659
1 TraesCS1B01G193100 chr1A 335828427 335832550 4123 False 1740.000000 2556 90.722500 5 2660 2 chr1A.!!$F1 2655
2 TraesCS1B01G193100 chr1D 267379101 267385115 6014 True 1116.666667 2309 89.736333 84 2660 3 chr1D.!!$R1 2576

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
785 826 0.247145 CGTCGTTGCCATCGCTTAAC 60.247 55.0 0.0 0.0 35.36 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2477 6119 1.094073 CCATTGCAGGAGCTTCGAGG 61.094 60.0 0.0 0.0 42.74 4.63 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
21 22 2.104331 CTACCCGCGCACTTCGAT 59.896 61.111 8.75 0.00 41.67 3.59
51 52 1.547820 CTGCCAGTGCACTCTTCTCTA 59.452 52.381 18.64 0.00 44.23 2.43
324 325 1.201181 GTTGCCATACACCGCATTGAA 59.799 47.619 0.00 0.00 34.35 2.69
330 331 1.598882 TACACCGCATTGAACTGCAA 58.401 45.000 0.00 0.00 42.40 4.08
333 334 0.311790 ACCGCATTGAACTGCAACTG 59.688 50.000 0.00 0.00 42.40 3.16
334 335 0.311790 CCGCATTGAACTGCAACTGT 59.688 50.000 0.00 0.00 42.40 3.55
335 336 1.401530 CGCATTGAACTGCAACTGTG 58.598 50.000 0.00 0.00 42.40 3.66
336 337 1.268692 CGCATTGAACTGCAACTGTGT 60.269 47.619 0.00 0.00 42.40 3.72
337 338 2.795681 CGCATTGAACTGCAACTGTGTT 60.796 45.455 0.00 0.00 42.40 3.32
339 340 3.618150 GCATTGAACTGCAACTGTGTTTT 59.382 39.130 0.00 0.00 41.87 2.43
341 342 5.552807 CATTGAACTGCAACTGTGTTTTTG 58.447 37.500 0.00 0.00 39.78 2.44
342 343 3.583806 TGAACTGCAACTGTGTTTTTGG 58.416 40.909 0.00 0.00 0.00 3.28
343 344 3.006323 TGAACTGCAACTGTGTTTTTGGT 59.994 39.130 0.00 0.00 0.00 3.67
346 347 2.923020 CTGCAACTGTGTTTTTGGTGTC 59.077 45.455 0.00 0.00 0.00 3.67
347 348 1.917303 GCAACTGTGTTTTTGGTGTCG 59.083 47.619 0.00 0.00 0.00 4.35
348 349 2.669950 GCAACTGTGTTTTTGGTGTCGT 60.670 45.455 0.00 0.00 0.00 4.34
349 350 3.168193 CAACTGTGTTTTTGGTGTCGTC 58.832 45.455 0.00 0.00 0.00 4.20
351 352 2.814919 ACTGTGTTTTTGGTGTCGTCAA 59.185 40.909 0.00 0.00 0.00 3.18
352 353 3.253677 ACTGTGTTTTTGGTGTCGTCAAA 59.746 39.130 0.00 0.00 32.96 2.69
354 355 2.918600 GTGTTTTTGGTGTCGTCAAACC 59.081 45.455 0.00 0.00 34.34 3.27
355 356 2.178783 GTTTTTGGTGTCGTCAAACCG 58.821 47.619 0.00 0.00 39.47 4.44
356 357 1.451067 TTTTGGTGTCGTCAAACCGT 58.549 45.000 0.00 0.00 39.47 4.83
357 358 1.451067 TTTGGTGTCGTCAAACCGTT 58.549 45.000 0.00 0.00 39.47 4.44
360 361 1.130749 TGGTGTCGTCAAACCGTTTTG 59.869 47.619 0.00 0.00 43.17 2.44
361 362 1.185189 GTGTCGTCAAACCGTTTTGC 58.815 50.000 0.00 0.00 41.78 3.68
362 363 1.088306 TGTCGTCAAACCGTTTTGCT 58.912 45.000 0.00 0.00 41.78 3.91
363 364 1.202087 TGTCGTCAAACCGTTTTGCTG 60.202 47.619 0.00 0.00 41.78 4.41
364 365 0.248296 TCGTCAAACCGTTTTGCTGC 60.248 50.000 0.00 0.00 41.78 5.25
365 366 0.248458 CGTCAAACCGTTTTGCTGCT 60.248 50.000 0.00 0.00 41.78 4.24
367 368 0.383949 TCAAACCGTTTTGCTGCTCC 59.616 50.000 0.00 0.00 41.78 4.70
464 478 0.605319 GGAGTGAACGCCATGGACAA 60.605 55.000 18.40 0.00 35.76 3.18
537 554 2.427453 ACAACAAGCTAGTCGATCGGAT 59.573 45.455 16.41 6.75 0.00 4.18
575 592 4.172505 GTTGTGTTTGTTTGCATGACAGA 58.827 39.130 0.00 0.00 0.00 3.41
576 593 3.768406 TGTGTTTGTTTGCATGACAGAC 58.232 40.909 13.99 13.99 33.95 3.51
577 594 3.192212 TGTGTTTGTTTGCATGACAGACA 59.808 39.130 17.59 17.59 41.33 3.41
578 595 3.792956 GTGTTTGTTTGCATGACAGACAG 59.207 43.478 20.34 0.00 43.58 3.51
599 616 3.570975 AGCAATGACTCAATCAAACAGCA 59.429 39.130 0.00 0.00 41.93 4.41
600 617 3.918591 GCAATGACTCAATCAAACAGCAG 59.081 43.478 0.00 0.00 41.93 4.24
601 618 4.482386 CAATGACTCAATCAAACAGCAGG 58.518 43.478 0.00 0.00 41.93 4.85
602 619 1.881973 TGACTCAATCAAACAGCAGGC 59.118 47.619 0.00 0.00 33.02 4.85
603 620 1.881973 GACTCAATCAAACAGCAGGCA 59.118 47.619 0.00 0.00 0.00 4.75
604 621 2.490903 GACTCAATCAAACAGCAGGCAT 59.509 45.455 0.00 0.00 0.00 4.40
605 622 3.689347 ACTCAATCAAACAGCAGGCATA 58.311 40.909 0.00 0.00 0.00 3.14
606 623 3.441572 ACTCAATCAAACAGCAGGCATAC 59.558 43.478 0.00 0.00 0.00 2.39
607 624 3.419943 TCAATCAAACAGCAGGCATACA 58.580 40.909 0.00 0.00 0.00 2.29
608 625 3.441222 TCAATCAAACAGCAGGCATACAG 59.559 43.478 0.00 0.00 0.00 2.74
609 626 1.167851 TCAAACAGCAGGCATACAGC 58.832 50.000 0.00 0.00 44.65 4.40
632 649 1.196354 GCGCATAATCAAGGCTAGCAG 59.804 52.381 18.24 5.87 0.00 4.24
681 698 8.738199 TTTATATGATCGACATAACGGAAGTC 57.262 34.615 10.39 0.00 43.47 3.01
697 714 1.067582 GTCCGTCTATGCTTCCCCG 59.932 63.158 0.00 0.00 0.00 5.73
699 716 2.280186 CGTCTATGCTTCCCCGGC 60.280 66.667 0.00 0.00 0.00 6.13
725 742 3.391296 ACCTGTGTCACTTTGGTGTCTAT 59.609 43.478 12.69 0.00 43.41 1.98
744 765 6.544197 TGTCTATGGTTTGCTTTAGTTGTTGA 59.456 34.615 0.00 0.00 0.00 3.18
748 769 9.260002 CTATGGTTTGCTTTAGTTGTTGAATTT 57.740 29.630 0.00 0.00 0.00 1.82
749 770 7.532682 TGGTTTGCTTTAGTTGTTGAATTTC 57.467 32.000 0.00 0.00 0.00 2.17
751 772 6.292114 GGTTTGCTTTAGTTGTTGAATTTCGG 60.292 38.462 0.00 0.00 0.00 4.30
753 774 5.897050 TGCTTTAGTTGTTGAATTTCGGTT 58.103 33.333 0.00 0.00 0.00 4.44
754 775 5.746245 TGCTTTAGTTGTTGAATTTCGGTTG 59.254 36.000 0.00 0.00 0.00 3.77
755 776 5.332280 GCTTTAGTTGTTGAATTTCGGTTGC 60.332 40.000 0.00 0.00 0.00 4.17
756 777 3.092334 AGTTGTTGAATTTCGGTTGCC 57.908 42.857 0.00 0.00 0.00 4.52
757 778 2.428890 AGTTGTTGAATTTCGGTTGCCA 59.571 40.909 0.00 0.00 0.00 4.92
758 779 3.069443 AGTTGTTGAATTTCGGTTGCCAT 59.931 39.130 0.00 0.00 0.00 4.40
762 803 4.279671 TGTTGAATTTCGGTTGCCATAAGT 59.720 37.500 0.00 0.00 0.00 2.24
769 810 1.727857 CGGTTGCCATAAGTTTGCGTC 60.728 52.381 0.00 0.00 0.00 5.19
776 817 1.069568 CATAAGTTTGCGTCGTTGCCA 60.070 47.619 0.00 0.00 0.00 4.92
779 820 1.792057 GTTTGCGTCGTTGCCATCG 60.792 57.895 0.00 0.00 0.00 3.84
782 823 3.788766 GCGTCGTTGCCATCGCTT 61.789 61.111 0.00 0.00 44.28 4.68
784 825 1.962092 GCGTCGTTGCCATCGCTTAA 61.962 55.000 0.00 0.00 44.28 1.85
785 826 0.247145 CGTCGTTGCCATCGCTTAAC 60.247 55.000 0.00 0.00 35.36 2.01
786 827 1.076332 GTCGTTGCCATCGCTTAACT 58.924 50.000 0.00 0.00 35.36 2.24
787 828 1.463444 GTCGTTGCCATCGCTTAACTT 59.537 47.619 0.00 0.00 35.36 2.66
805 864 2.819608 ACTTAAGTTCAGCCCGTACGTA 59.180 45.455 15.21 0.00 0.00 3.57
816 875 3.498840 CGTACGTACGGTAGCACTC 57.501 57.895 34.54 1.44 45.30 3.51
847 933 1.743772 GCAGGGCGCAAGAAAGAGATA 60.744 52.381 10.83 0.00 41.79 1.98
848 934 2.843701 CAGGGCGCAAGAAAGAGATAT 58.156 47.619 10.83 0.00 43.02 1.63
849 935 3.209410 CAGGGCGCAAGAAAGAGATATT 58.791 45.455 10.83 0.00 43.02 1.28
851 937 3.879892 AGGGCGCAAGAAAGAGATATTTC 59.120 43.478 10.83 0.00 39.09 2.17
863 4496 1.421646 AGATATTTCTTCTGGGGCCGG 59.578 52.381 0.00 0.00 0.00 6.13
865 4498 2.279037 TATTTCTTCTGGGGCCGGCC 62.279 60.000 38.57 38.57 0.00 6.13
947 4580 2.228822 GCCCATGGCGATAAGGTTATTG 59.771 50.000 6.09 0.00 39.62 1.90
955 4588 3.713288 CGATAAGGTTATTGCCACGAGA 58.287 45.455 0.00 0.00 0.00 4.04
956 4589 3.736252 CGATAAGGTTATTGCCACGAGAG 59.264 47.826 0.00 0.00 0.00 3.20
1041 4678 3.791586 GCTCTCCAGCCCCCTCAC 61.792 72.222 0.00 0.00 40.14 3.51
1042 4679 3.086600 CTCTCCAGCCCCCTCACC 61.087 72.222 0.00 0.00 0.00 4.02
1043 4680 4.741239 TCTCCAGCCCCCTCACCC 62.741 72.222 0.00 0.00 0.00 4.61
1053 4690 2.784654 CCCTCACCCCACCCCAAAA 61.785 63.158 0.00 0.00 0.00 2.44
1054 4691 1.234529 CCTCACCCCACCCCAAAAA 59.765 57.895 0.00 0.00 0.00 1.94
1056 4693 1.075151 TCACCCCACCCCAAAAACC 60.075 57.895 0.00 0.00 0.00 3.27
1062 4699 1.655372 CCACCCCAAAAACCCATCAT 58.345 50.000 0.00 0.00 0.00 2.45
1064 4701 1.554617 CACCCCAAAAACCCATCATCC 59.445 52.381 0.00 0.00 0.00 3.51
1066 4703 2.225856 ACCCCAAAAACCCATCATCCAT 60.226 45.455 0.00 0.00 0.00 3.41
1079 4716 4.758251 TCCATGGACGCACAGCCG 62.758 66.667 11.44 0.00 0.00 5.52
1098 4735 2.125106 GCCACCACGTCCATCCTC 60.125 66.667 0.00 0.00 0.00 3.71
1101 4738 1.139734 CACCACGTCCATCCTCTCG 59.860 63.158 0.00 0.00 0.00 4.04
1102 4739 2.052690 ACCACGTCCATCCTCTCGG 61.053 63.158 0.00 0.00 0.00 4.63
1108 4745 2.060383 TCCATCCTCTCGGCACCTG 61.060 63.158 0.00 0.00 0.00 4.00
1575 5215 2.203938 AGCTGGGACCCGGAGAAA 60.204 61.111 24.69 0.00 29.82 2.52
1644 5284 2.481104 GCTGTGGAAGGAAGAGATCGAG 60.481 54.545 0.00 0.00 0.00 4.04
1824 5464 2.195922 CAAAACTGAACACTTGGCAGC 58.804 47.619 0.00 0.00 33.03 5.25
1830 5470 3.118665 ACTGAACACTTGGCAGCAAAAAT 60.119 39.130 0.00 0.00 33.03 1.82
1842 5482 4.810491 GGCAGCAAAAATGAGAAAACTGAA 59.190 37.500 0.00 0.00 0.00 3.02
1857 5497 2.440247 GAATGAACCCCCAGGCCG 60.440 66.667 0.00 0.00 36.11 6.13
2072 5712 9.321562 AGAACTGTTTATTTTCGAGTTAGTCAA 57.678 29.630 0.00 0.00 0.00 3.18
2075 5715 8.504005 ACTGTTTATTTTCGAGTTAGTCAATGG 58.496 33.333 0.00 0.00 0.00 3.16
2076 5716 7.302524 TGTTTATTTTCGAGTTAGTCAATGGC 58.697 34.615 0.00 0.00 0.00 4.40
2077 5717 7.041030 TGTTTATTTTCGAGTTAGTCAATGGCA 60.041 33.333 0.00 0.00 0.00 4.92
2078 5718 5.551760 ATTTTCGAGTTAGTCAATGGCAG 57.448 39.130 0.00 0.00 0.00 4.85
2079 5719 3.678056 TTCGAGTTAGTCAATGGCAGT 57.322 42.857 0.00 0.00 0.00 4.40
2081 5721 2.002586 CGAGTTAGTCAATGGCAGTGG 58.997 52.381 15.62 0.00 0.00 4.00
2082 5722 2.353704 CGAGTTAGTCAATGGCAGTGGA 60.354 50.000 15.62 0.00 0.00 4.02
2085 5725 4.666512 AGTTAGTCAATGGCAGTGGAAAT 58.333 39.130 15.62 3.92 0.00 2.17
2106 5746 7.093333 GGAAATTTCCTGGTCCAGAACATTAAT 60.093 37.037 26.94 7.23 44.11 1.40
2124 5764 6.951198 ACATTAATGGGTCCTGTTTTGTGATA 59.049 34.615 19.37 0.00 0.00 2.15
2161 5803 0.616371 TTACCATTGACGGGGACAGG 59.384 55.000 0.00 0.00 0.00 4.00
2202 5844 7.197703 TCTTAAATATTGCTGTCATGTGCATG 58.802 34.615 5.86 5.86 39.07 4.06
2300 5942 1.078143 GCGTCCAGCTCTCCCAAAT 60.078 57.895 0.00 0.00 44.04 2.32
2348 5990 3.965347 AGCTCCGCCTTCTTATTAACCTA 59.035 43.478 0.00 0.00 0.00 3.08
2406 6048 6.449635 TCGGCAATCTACATAAAGCATTTT 57.550 33.333 0.00 0.00 40.09 1.82
2574 6224 3.377798 AGATCGAACGAAAGAGGAGTACC 59.622 47.826 0.12 0.00 0.00 3.34
2586 6236 5.313280 AGAGGAGTACCAGATACACTAGG 57.687 47.826 0.00 0.00 38.94 3.02
2601 6255 9.819267 AGATACACTAGGACTTATTTTAAGCAC 57.181 33.333 0.00 0.00 0.00 4.40
2605 6259 8.100791 ACACTAGGACTTATTTTAAGCACATCA 58.899 33.333 0.00 0.00 0.00 3.07
2612 6266 9.807649 GACTTATTTTAAGCACATCATGGAATT 57.192 29.630 0.00 0.00 0.00 2.17
2622 6276 6.319658 AGCACATCATGGAATTAAGTTGGTAG 59.680 38.462 0.00 0.00 0.00 3.18
2631 6285 7.718525 TGGAATTAAGTTGGTAGTTTTCAACC 58.281 34.615 0.00 0.00 42.87 3.77
2632 6286 7.342284 TGGAATTAAGTTGGTAGTTTTCAACCA 59.658 33.333 0.00 0.00 43.99 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.375013 GAAGTGCGCGGGTAGGAAA 60.375 57.895 8.83 0.00 0.00 3.13
1 2 2.263540 GAAGTGCGCGGGTAGGAA 59.736 61.111 8.83 0.00 0.00 3.36
2 3 4.124351 CGAAGTGCGCGGGTAGGA 62.124 66.667 8.83 0.00 0.00 2.94
3 4 3.426117 ATCGAAGTGCGCGGGTAGG 62.426 63.158 8.83 0.00 40.61 3.18
51 52 3.933861 AAGTTCAGTTCCACTTCCACT 57.066 42.857 0.00 0.00 0.00 4.00
324 325 2.298729 ACACCAAAAACACAGTTGCAGT 59.701 40.909 0.00 0.00 0.00 4.40
330 331 2.428491 TGACGACACCAAAAACACAGT 58.572 42.857 0.00 0.00 0.00 3.55
333 334 2.918600 GGTTTGACGACACCAAAAACAC 59.081 45.455 0.00 0.00 35.57 3.32
334 335 2.414293 CGGTTTGACGACACCAAAAACA 60.414 45.455 0.00 0.00 35.57 2.83
335 336 2.178783 CGGTTTGACGACACCAAAAAC 58.821 47.619 0.00 0.00 35.57 2.43
336 337 1.811359 ACGGTTTGACGACACCAAAAA 59.189 42.857 0.00 0.00 35.57 1.94
337 338 1.451067 ACGGTTTGACGACACCAAAA 58.549 45.000 0.00 0.00 35.57 2.44
339 340 1.451067 AAACGGTTTGACGACACCAA 58.549 45.000 5.12 0.00 37.61 3.67
341 342 1.817609 CAAAACGGTTTGACGACACC 58.182 50.000 21.39 0.00 45.99 4.16
342 343 1.185189 GCAAAACGGTTTGACGACAC 58.815 50.000 29.42 6.67 45.99 3.67
343 344 1.088306 AGCAAAACGGTTTGACGACA 58.912 45.000 29.42 0.00 45.99 4.35
346 347 0.248458 AGCAGCAAAACGGTTTGACG 60.248 50.000 29.42 18.71 45.99 4.35
347 348 1.477105 GAGCAGCAAAACGGTTTGAC 58.523 50.000 29.42 19.19 45.99 3.18
348 349 0.383949 GGAGCAGCAAAACGGTTTGA 59.616 50.000 29.42 0.00 45.99 2.69
349 350 0.102120 TGGAGCAGCAAAACGGTTTG 59.898 50.000 21.60 21.60 45.88 2.93
351 352 0.314935 CATGGAGCAGCAAAACGGTT 59.685 50.000 0.00 0.00 0.00 4.44
352 353 1.959085 CATGGAGCAGCAAAACGGT 59.041 52.632 0.00 0.00 0.00 4.83
354 355 4.157817 GCATGGAGCAGCAAAACG 57.842 55.556 0.00 0.00 44.79 3.60
464 478 2.283529 ACAGCCATTCGTCCGTCCT 61.284 57.895 0.00 0.00 0.00 3.85
516 530 1.816835 TCCGATCGACTAGCTTGTTGT 59.183 47.619 18.66 3.50 0.00 3.32
517 531 2.561733 TCCGATCGACTAGCTTGTTG 57.438 50.000 18.66 9.07 0.00 3.33
518 532 2.952978 AGATCCGATCGACTAGCTTGTT 59.047 45.455 18.66 0.00 0.00 2.83
537 554 3.134081 ACACAACCGGAGAAGAAAAGAGA 59.866 43.478 9.46 0.00 0.00 3.10
575 592 4.558095 GCTGTTTGATTGAGTCATTGCTGT 60.558 41.667 0.00 0.00 36.54 4.40
576 593 3.918591 GCTGTTTGATTGAGTCATTGCTG 59.081 43.478 0.00 0.00 36.54 4.41
577 594 3.570975 TGCTGTTTGATTGAGTCATTGCT 59.429 39.130 0.00 0.00 36.54 3.91
578 595 3.904571 TGCTGTTTGATTGAGTCATTGC 58.095 40.909 0.00 0.00 36.54 3.56
601 618 1.577328 ATTATGCGCCGGCTGTATGC 61.577 55.000 26.68 20.47 40.82 3.14
602 619 0.443869 GATTATGCGCCGGCTGTATG 59.556 55.000 26.68 9.69 40.82 2.39
603 620 0.034756 TGATTATGCGCCGGCTGTAT 59.965 50.000 26.68 23.09 40.82 2.29
604 621 0.179070 TTGATTATGCGCCGGCTGTA 60.179 50.000 26.68 17.82 40.82 2.74
605 622 1.439353 CTTGATTATGCGCCGGCTGT 61.439 55.000 26.68 12.61 40.82 4.40
606 623 1.280746 CTTGATTATGCGCCGGCTG 59.719 57.895 26.68 19.05 40.82 4.85
607 624 1.893808 CCTTGATTATGCGCCGGCT 60.894 57.895 26.68 8.66 40.82 5.52
608 625 2.639286 CCTTGATTATGCGCCGGC 59.361 61.111 19.07 19.07 40.52 6.13
609 626 0.602638 TAGCCTTGATTATGCGCCGG 60.603 55.000 4.18 0.00 0.00 6.13
613 630 2.487934 ACTGCTAGCCTTGATTATGCG 58.512 47.619 13.29 0.00 0.00 4.73
681 698 2.421739 CCGGGGAAGCATAGACGG 59.578 66.667 0.00 0.00 35.01 4.79
683 700 1.523938 GTGCCGGGGAAGCATAGAC 60.524 63.158 2.18 0.00 43.29 2.59
725 742 6.254589 CGAAATTCAACAACTAAAGCAAACCA 59.745 34.615 0.00 0.00 0.00 3.67
744 765 3.993736 GCAAACTTATGGCAACCGAAATT 59.006 39.130 0.00 0.00 0.00 1.82
748 769 0.519519 CGCAAACTTATGGCAACCGA 59.480 50.000 0.00 0.00 0.00 4.69
749 770 0.239879 ACGCAAACTTATGGCAACCG 59.760 50.000 0.00 0.00 0.00 4.44
751 772 1.069500 ACGACGCAAACTTATGGCAAC 60.069 47.619 0.00 0.00 0.00 4.17
753 774 1.069568 CAACGACGCAAACTTATGGCA 60.070 47.619 0.00 0.00 0.00 4.92
754 775 1.602191 CAACGACGCAAACTTATGGC 58.398 50.000 0.00 0.00 0.00 4.40
755 776 1.602191 GCAACGACGCAAACTTATGG 58.398 50.000 0.00 0.00 0.00 2.74
756 777 1.069568 TGGCAACGACGCAAACTTATG 60.070 47.619 0.00 0.00 42.51 1.90
757 778 1.231221 TGGCAACGACGCAAACTTAT 58.769 45.000 0.00 0.00 42.51 1.73
758 779 1.195900 GATGGCAACGACGCAAACTTA 59.804 47.619 0.00 0.00 42.51 2.24
762 803 2.553770 CGATGGCAACGACGCAAA 59.446 55.556 12.11 0.00 42.51 3.68
769 810 3.124636 ACTTAAGTTAAGCGATGGCAACG 59.875 43.478 20.31 13.18 43.41 4.10
780 821 4.325472 CGTACGGGCTGAACTTAAGTTAAG 59.675 45.833 23.65 23.65 39.11 1.85
782 823 3.255642 ACGTACGGGCTGAACTTAAGTTA 59.744 43.478 20.58 8.68 38.56 2.24
784 825 1.615392 ACGTACGGGCTGAACTTAAGT 59.385 47.619 21.06 1.12 0.00 2.24
785 826 2.358939 ACGTACGGGCTGAACTTAAG 57.641 50.000 21.06 0.00 0.00 1.85
786 827 2.414029 CGTACGTACGGGCTGAACTTAA 60.414 50.000 34.54 0.00 45.30 1.85
787 828 1.130373 CGTACGTACGGGCTGAACTTA 59.870 52.381 34.54 0.00 45.30 2.24
805 864 0.739813 GAAATGGCGAGTGCTACCGT 60.740 55.000 0.00 0.00 42.25 4.83
812 871 0.169672 CCTGCTTGAAATGGCGAGTG 59.830 55.000 0.00 0.00 0.00 3.51
816 875 2.182537 GCCCTGCTTGAAATGGCG 59.817 61.111 0.00 0.00 31.55 5.69
847 933 2.043953 GCCGGCCCCAGAAGAAAT 60.044 61.111 18.11 0.00 0.00 2.17
848 934 4.360405 GGCCGGCCCCAGAAGAAA 62.360 66.667 36.64 0.00 0.00 2.52
872 4505 2.282180 CGTTCCTGGGTTGGGTGG 60.282 66.667 0.00 0.00 0.00 4.61
909 4542 2.510411 CAGTGGTCAGTGGTGGCA 59.490 61.111 0.00 0.00 0.00 4.92
942 4575 0.830648 CTCCCCTCTCGTGGCAATAA 59.169 55.000 0.00 0.00 0.00 1.40
947 4580 3.844090 GCTCTCCCCTCTCGTGGC 61.844 72.222 0.00 0.00 0.00 5.01
955 4588 2.757917 GACGAGCTGCTCTCCCCT 60.758 66.667 25.59 4.48 38.62 4.79
956 4589 4.200283 CGACGAGCTGCTCTCCCC 62.200 72.222 25.59 11.54 38.62 4.81
1036 4673 1.118965 GTTTTTGGGGTGGGGTGAGG 61.119 60.000 0.00 0.00 0.00 3.86
1037 4674 1.118965 GGTTTTTGGGGTGGGGTGAG 61.119 60.000 0.00 0.00 0.00 3.51
1038 4675 1.075151 GGTTTTTGGGGTGGGGTGA 60.075 57.895 0.00 0.00 0.00 4.02
1039 4676 2.144078 GGGTTTTTGGGGTGGGGTG 61.144 63.158 0.00 0.00 0.00 4.61
1040 4677 1.979389 ATGGGTTTTTGGGGTGGGGT 61.979 55.000 0.00 0.00 0.00 4.95
1041 4678 1.151921 ATGGGTTTTTGGGGTGGGG 60.152 57.895 0.00 0.00 0.00 4.96
1042 4679 0.472734 TGATGGGTTTTTGGGGTGGG 60.473 55.000 0.00 0.00 0.00 4.61
1043 4680 1.554617 GATGATGGGTTTTTGGGGTGG 59.445 52.381 0.00 0.00 0.00 4.61
1044 4681 1.554617 GGATGATGGGTTTTTGGGGTG 59.445 52.381 0.00 0.00 0.00 4.61
1045 4682 1.150986 TGGATGATGGGTTTTTGGGGT 59.849 47.619 0.00 0.00 0.00 4.95
1062 4699 4.758251 CGGCTGTGCGTCCATGGA 62.758 66.667 11.44 11.44 0.00 3.41
1079 4716 4.796495 GGATGGACGTGGTGGCCC 62.796 72.222 0.00 0.00 0.00 5.80
1080 4717 3.682292 GAGGATGGACGTGGTGGCC 62.682 68.421 0.00 0.00 0.00 5.36
1081 4718 2.125106 GAGGATGGACGTGGTGGC 60.125 66.667 0.00 0.00 0.00 5.01
1192 4829 1.029408 TTGTTGCTTGTGCTGTCCGT 61.029 50.000 0.00 0.00 40.48 4.69
1824 5464 7.041848 GGGGTTCATTCAGTTTTCTCATTTTTG 60.042 37.037 0.00 0.00 0.00 2.44
1830 5470 3.117322 TGGGGGTTCATTCAGTTTTCTCA 60.117 43.478 0.00 0.00 0.00 3.27
1857 5497 3.609853 TCATCAGTGTTGTATTCTGGCC 58.390 45.455 0.00 0.00 0.00 5.36
1892 5532 4.384537 CCATCCATCTGCTTTAGGAGAACA 60.385 45.833 5.04 0.00 45.49 3.18
2055 5695 6.092122 CACTGCCATTGACTAACTCGAAAATA 59.908 38.462 0.00 0.00 0.00 1.40
2056 5696 5.003804 ACTGCCATTGACTAACTCGAAAAT 58.996 37.500 0.00 0.00 0.00 1.82
2081 5721 5.728637 AATGTTCTGGACCAGGAAATTTC 57.271 39.130 21.56 9.83 31.51 2.17
2082 5722 7.310609 CCATTAATGTTCTGGACCAGGAAATTT 60.311 37.037 21.44 10.15 31.38 1.82
2085 5725 5.016173 CCATTAATGTTCTGGACCAGGAAA 58.984 41.667 21.56 8.63 31.38 3.13
2106 5746 6.739331 ATTTTTATCACAAAACAGGACCCA 57.261 33.333 0.00 0.00 0.00 4.51
2151 5791 3.249189 ATGCACACCTGTCCCCGT 61.249 61.111 0.00 0.00 0.00 5.28
2193 5835 4.749976 TGAATCACCATTTCATGCACATG 58.250 39.130 4.18 4.18 40.09 3.21
2202 5844 5.916318 TGCCCATTTATGAATCACCATTTC 58.084 37.500 0.00 0.00 0.00 2.17
2213 5855 5.136068 TCCTTTGGTATGCCCATTTATGA 57.864 39.130 0.00 0.00 44.74 2.15
2300 5942 2.689553 TGCCAGTCATGCTTTCGATA 57.310 45.000 0.00 0.00 0.00 2.92
2469 6111 3.712187 CAGGAGCTTCGAGGAGTTTATC 58.288 50.000 0.00 0.00 0.00 1.75
2477 6119 1.094073 CCATTGCAGGAGCTTCGAGG 61.094 60.000 0.00 0.00 42.74 4.63
2549 6191 5.838531 ACTCCTCTTTCGTTCGATCTATT 57.161 39.130 0.00 0.00 0.00 1.73
2550 6192 5.239087 GGTACTCCTCTTTCGTTCGATCTAT 59.761 44.000 0.00 0.00 0.00 1.98
2551 6193 4.574013 GGTACTCCTCTTTCGTTCGATCTA 59.426 45.833 0.00 0.00 0.00 1.98
2557 6207 4.722361 ATCTGGTACTCCTCTTTCGTTC 57.278 45.455 0.00 0.00 34.23 3.95
2562 6212 6.068971 TCCTAGTGTATCTGGTACTCCTCTTT 60.069 42.308 0.00 0.00 34.27 2.52
2568 6218 8.694581 AATAAGTCCTAGTGTATCTGGTACTC 57.305 38.462 0.00 0.00 34.27 2.59
2574 6224 9.817809 TGCTTAAAATAAGTCCTAGTGTATCTG 57.182 33.333 0.00 0.00 0.00 2.90
2586 6236 9.807649 AATTCCATGATGTGCTTAAAATAAGTC 57.192 29.630 0.00 0.00 0.00 3.01
2601 6255 9.573133 GAAAACTACCAACTTAATTCCATGATG 57.427 33.333 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.